Caret 5 Changes
Version 5.62 (14 Feb 2011)
- (10 Feb 2011) Update the PALS coordinate files used to map
volumes to surfaces to correct the coordinate system origin.
Version 5.616 (12 Nov 2010)
- (12 Nov 2010) Add warning message to Ubuntu distribution of Caret
(which we do not build that it contains reduced functionality and may
not operate properly due to its use of incompatible versions of
third-party libraries).
- (12 Nov 2010) Fixed calculation of P-Values in statistical
tests. The index into the randomized clusters was off by one or
two.
- (11 Nov 2010) Changed cortical folding SI calculation to use
atan2() instead of atan().
Version 5.615 (26 July 2010)
- (16 Sep 2010) Updated caret file name regular expressions so that
it supports new node number convention such as "164k_fs_LR".
- (10 Sep 2010) Trying to fix problem with paint label editing that
is apparently a problem with keeping GIFTI paint files and area colors
synchronized.
- (10 Sep 2010) Fixed failure of resample spec file command caused
by 08 Sep change.
- (08 Sep 2010) Fix create deformation map command for occurrance
of both sphere not having the center of the sphere at the origin.
- (30 Aug 2010) Fixed a bug in registration algorithms that was
resampling each border many times (equal to number of points in the
border).
- (20 Aug 2010) Updated 711 volume origins.
- (12 Aug 2010) Changed Volume Menu->Paint->Generate Colors
for Paints Without Colors to also generate paint names for voxel
indices that do not have a name.
- (26 July 2010) Added the ability to read metric files in GIFTI
format that contain two-dimensional MxN) arrays. After the file
is read, N M-dimensional arrays replace the MxN array.
- (01 July 2010) Added "caret-command -surface-border-file-merge"
which merges border projection file.
- (29 June 2010) Added "caret_command_test -surface-normals" which
places a surface's normal vectors into a GIFTI vector file.
- (28 June 2010) Added "caret_command -paint-label-name-update"
which removes prefixes and suffixes from paint label names. A
suffix starts with the last period of the label name and a prefix ends
with the first period in the label name.
- (28 June 2010) Added "caret_command -paint-set-column-name" to
set the names of column in paint files.
- (25 June 2010) Curvature calculation was setting K1 to the
principal curvature with the greatest absolute value. K1is now
the greatest value of the principal curvatures.
- (18 June 2010) Added "Multi-Res Morph Parameters File" that
stores the parameters used during multi-resolution morphing. It
can be loaded and saved in the GUI and added as an option to the
command line multi-resolution morphing.
- (18 June 2010) Added buttons to remove prefixes and suffixes from
paint names to the Edit Paint Names dialog.
- (14 June 2010) Fixed reading of GIFTI files with array order set
to column-major order.
- (26 May 2010) Changed caret_source/caret_qmake_include.pro.
Any references to environment variables for includes or libraries were
changed to add a second "$", eg: $$(VTK_INC_DIR) instead of
$(VTK_INC_DIR). This results in the VALUE of the environment
variable being placed in the Makefile instead of the the environment
variable itself. This eliminates the need to define environment
variables in integrated development environments (Eclipse, XCode, etc).
- (24 May 2010) Added surface area for each node to folding
measurements metric file.
- (20 May 2010) Added optional metric file output to folding
measurments on Surface ROI Dialog and command line. The metric
file, on output, contains folding measurements at each node.
- (26 April 2010) Fixed drawing of 3D symbols (unidirectional
arrow/cylinder) for surface vectors when the vector's Z component was
near zero.
- (22 April 2010) Fixed reading of FreeSurfer binary format patch
surface files.
- (22 April 2010) After reading a Surface File, update the selected
topology files.
- (21 April 2010) Added an additional step to the operation that
generates the cerebral hull volume from the segmentation volume.
In some cases with deep/large sulci, a small hole was present after the
dilation operation and this hole was opened up during the erosion
operation resulting in a "deep cave" in the cerebral hull volume and
surface. This has been corrected by filling any cavities that are
present after the dilation operation but prior to the erosion operation.
- (21 April 2010) Fixed help information for "caret_command
-volume-erode" command.
- (21 April 2010) Fixed "caret_command
-volume-segmentation-to-cerebral-hull " which was mistakenly reading
the hull volume as the segmentation volume.
- (14 April 2010) Fixed surface to segmentation volume conversion
(caret_command -surface-to-segmentation-volume) that failed to
sometimes work properly. It turns out if the coordinate file was
a left hemisphere and its structure tag in the header did not identify
it as a left hemisphere, the code that filled the inside of the
segmentation volume failed.
- (14 April 2010) Added "caret_command
-deformation-map-apply-generic-names" which applies a deformation map
to a data file but allows the user to override the source and target
files (coord/topo) contained in the deformation map file.
- (13 April 2010) When reading a GIFTI file, check the type of the
data arrays and convert them if necessary. For example, a metric
data file should have all of its data arrays at float data arrays and
Paint file should have integer data arrays.
- (30 March 2010) Remove all volume files prior to loading a scene.
- (29 March 2010) Fixed reading of study metadata link from NIFTI
volumes.
- (09 March 2010) Fixed reading of GIFTI label files with colors
included in the labels.
- (05 March 2010) Display an error message if trying to import free
surfer label files and none are found.
- (05 March 2010) Fixed reading of column comments from gifti data
array files.
- (03 March 2010) Changed caret6 spec file conversion so that it
ignores separate volume data files (*.img).
- (01 March 2010) Fixed color assignment for paint files when paint
file was read but lacked colors. This fix is related to 01 Dec
2009 GIFTI label table update.
- (22 Feb 2010) Changed Landmark-Vector-Difference spherical
registartion so that when createing the source deformed coordinate
file, it only flips the coordinates if it is the first cycle of the
first stage when the source and target are different hemispheres.
- (17 Feb 2010) Fixed scaling of surfaces to match the surface area
of another surface. Normally, this is run when creating inflated
and other surfaces from the fiducial surface.
- (10Feb 2010) Changed version to
5.614.
- (10 Feb 2010) Fixed writing of NIFTI volumes with data type of
signed 8-bit integer and the data value was greater than 127.
- (10 Feb 2010) When converting a paint column to a paint volume,
add all of the paint labels to the volume file, even those that are
unused, so that the paint file and the paint volume use the same
indices for the same label.
- (10 Feb 2010) Added a new Caret extension to the NIFTI volume
file. Caret had used an extension of the AFNI extension but
additional data did not fit well into the AFNI extension. At this
time, Caret still writes the AFNI extension so that the files will
function with older versions of caret.
- (09 Feb 2010) Rewrote cleanup of paint names to make it much
faster. This was needed because GIFTI files may have a few,
large, sparse indexed labels which creates an enormouse label table
with a million empty entries. The alternative, rewriting the way
labels are handled in Caret, is too ginormous of a change.
- (26 Jan 2010) Changed version
to 5.613.
- (26 Jan 2010) Use a new set of deformation spheres for the
Landmark Vector Difference deformation algorithm.
- (25 Jan 2010) Fixed bug related to 18 Dec 2009. When the
corpus callosum volume was supplied as the anatomy volume the extent of
the corpus callosum was not determined causing the medial wall border
to fail.
- (05 Jan 2010) Add endpoint factor for multistage vector
deformation.
- (05 Jan 2010) Fixed problems with border resmapling value on
Deformation Dialog and proper saving to deformation map file.
- (05 Jan 2010) Show variance when editing border file through
Deformation Dialog.
- (05 Jan 2010) When printing crossover message from Surface Vector
Deformation, start at one instead of zero.
- (05 Jan 2010) Fixed bug with last change that uses the remote ID
for nodes so that when a scene is loaded, it does not try to display
text for all of the nodes in the paint cluster auto loader region.
- (04 Jan 2010) Show identification symbols over the paint cluster
auto loader paint region.
- (04 Jan 2010) Fixed problem with the metric palette colorbar
failing to display when surfaces were displayed.
- (18 Dec 2009) If the input volume file name to auto-landmarks
contains "corpus" and "callosum" use it as the corpus callosum instead
of extracting the corpus callosum from the anatomy volume.
- (01 Dec 2009) Fixed crash that occurred when reading a FreeSurfer
binary patch file. The patch file format seems to have been
changed. However, the new format is unknown so the best that can
be done is to prevent the crash and display an error message.
- (01 Dec 2009) Fixed writing of GIFTI Label file from Caret5 so
that the label table has its colors assigned (provided the area color
file is loaded).
- (01 Dec 2009) Added an "-area-color-file" option to
"caret_command -file-convert -area-color-file name.areacolor
-format-convert" so that output GIFTI label files can receive colors.
- (18 Nov 2009) Do not draw backfacing triangles when drawing foci
as 3D shapes. Otherwise, if the foci opacity is less than one,
the foci have a "half moon" appearance.
- (16 Nov 2009) Save contour scaling in the contour file so that
scaling is preserved for any future contour drawing.
- (13 Nov 2009) Draw surface foci before drawing the surface so
that the foci can be seen through a transparent surface.
- (12 Nov 2009) Added a vector drawing mode that draws
unidirectional vectors without an arrowhead.
- (05 Nov 2009) Fixed failure in automatic border drawing. If
orbital sulcus is not found when creating the frontal cut, try to find
the transverse orbital sulcus. If neither are found, approximate
a coordinate where the orbital sulcus should be.
- (02 Nov 2009) Fixed dialog for setting the contour section
spacing. It was always displaying the wrong value but the value
entered by the user was properly processed.
- (05 Oct 2009) Fixed bug with caret_command
-surface-foci-projection. It was not properly processing the
"-project-onto-surface" option.
- (05 Oct 2009) Fixed bug with foci unprojection that occurred when
a focus projected to a node instead of a tile. Fixing the problem
required calculating the surface normal for the node since the tile
normal was all zeros.
- (28 Sep 2009) Fixed error that determined the structure of the
very inflated surface during probabilistic sulcal identification.
This bug was preventing the command line automatic border generation
from functioning correctly.
- (23 Sep 2009) Changed version
to 5.612.
- (09 Sep 2009) Fixed quaternion parameter for NIFTI volumes with a
valid qform code.
- (09 Sep 2009) Fixed use of structure in caret_command
-file-convert -sc.
- (02 Sep 2009) Changed Vector Settings Functional Volume to use
the values as negative and positive thresholds.
- (31 Aug 2009) Added cluster auto loaders to Connectivity Dialog.
- (31 Aug 2009) Fixed crash that occurred if the user tried to map
foci to the PALS atlas with caret installed improperly so that the PALS
atlas files cannot be found.
- (31 Aug 2009) Fixes for paint dilation and metric/functional
volume auto loader crashes. On the Display Control's Vector
Settings page, keep the functional volume mask set to the last loaded
functional volume if the selected functional volume becomes invalid.
- (25 Aug 2009) Added functional volume masking to Display
Control's Vector Settings page.
- (25 Aug 2009) Added "caret_command -paint-dilation" which dilates
paints.
- (24 Aug 2009) Added "caret_command -surface-border-to-paint"
which assigns border names to nodes that are nearest to a link in the
border.
- (24 Aug 2009) Implemented limit of vector display to those within
an angle of an orthogonal axis.
- (24 Aug 2009) Functional volume auto loader and multiple metric
auto loaders now working and working with scenes.
- (21 Aug 2009) Metric auto loaders now work with scenes.
Changed some default settings for the Display Control's vector settings
page.
- (19 Aug 2009) On Display Control's Metric Setting's page, add
Auto Scale - Percentage. This new mode maps the metric values to
percentages of the min/max positive/negative values.
- (19 Aug 2009) Moved metric auto loading (4 metric auto loaders)
from Display Control to the new Connectivity Dialog. The dialog
is launched using the Attributes->Connectivity menu item.
- (18 Aug 2009) Metric auto loading is now triggered by clicking on
a volume slice or in Surface & Volume surface and slices.s
- (14 Aug 2009) Fixed reading of a volume border file using File
Menu->Open Data File.
- (14 Aug 2009) Fixed writing of AFNI headers so that coordinates
and spacing are always the weird RAI even though the data is LPI.
- (10 Aug 2009) Print additional information if surface
registration failed due to a problem with a landmark border file.
- (04 Aug 2009) Changed effect of surface clipping on
vectors. Vectors are displayed when there origin (arrows) or
center (oriented) is within the clipping planes. The clipping
planes no longer remove parts of vectors. Each vector file is now
maintained separately in memory and the display of each vector file is
controlled on the Display Control's Vector Selection page. Fixed
update of the segmentation volume selection control on the Vector
Settings page.
- (30 July 2009) Fixed reading of GIFTI files with data stored in
an external file and data arrays without a "data" tag.
- (29 July 2009) Vector Changes: Reduced number of polygons used to
draw cylinders and cones. Split vector volume slice thickness
into distance above and below the slice. Added magnitude
threshold to Display Control's Vector Settings page. Added a
coloring mode that draws using the colors assigned to the vector or
applies the vector's XYZ-unit vector as a red, green, and blue color
components. Add optional use of segmentation volume that is used
as a mask to limit the display of vectors.
- (28 July 2009) Renamed "caret_command -volume-to-vector" to
"caret_command -volume-fsl-to-vector". It now requires a volume
in the output space and correctly builds and applies the FSL transform
so that the resulting vectors are in the output space. An option
allows the user to save the created transformation matrix.
- (27 July 2009) Added Surface line width and volume slice
thickness to the Display Control's Surface Vector page.
- (27 July 2009) Changed reading of NIFTI volume file header data.
- (16 July 2009) Added new surface drawing modes for vectors that
draw the vectors as lines. This is needed because the 3D arrows
and cylinders can take a long time to draw, especially if there are
many of them.
- (16 July 2009) Added new Surface Clipping page to the Display
Control. Surface clipping allows one to inhibit the display of a
surface and its data for all six axis (negative and positive X, Y, and
Z). Partial View was removed from the Surface Miscellaneous page
since Surface Clipping can provide the same functionality.
- (15 July 2009) Incorporated Tim's automatic landmark
identification updates.
- (15 July 2009) Replaced the surface vector file with VectorFile
which is in GIFTI format. Replace Display Control's Surface
Vector Settings page with Vector Settings Page. Eliminated
Display Control's Surface Vector Selection page. The new vectors
are displayed on both surfaces and volumes.
- (15 July 2009) Added "caret_command -volume-to-vector" which
converts vector data, produced by BEDPOST and stored in volume files,
into VectorFiles.
- (08 July 2009) Renamed the "VectorFile" used only during SureFit
operations to "SureFitVectorFile".
- (07 July 2009) Fixed problem with the preferences file being
written to the current directory instead of the user's home
directory. This error only occurred if the user did not have an
existing preferences file in his/her home directory.
- (06 July 2009) Fixed error caused by printing help information
for the command "caret_command -surface-border-landmark-identification".
- (02 July 2009) Added "caret_command -spec-file-change-resolution"
which changes the resolution of surface data files in a spec file.
- (01 July 2009) Fixed linking of cell and foci projection files
when deforming data files.
- (29 June 2009) Have "caret_command -volume-euler-count" exit with
a message indicating that "-volume-topology-report" should be used
instead.
- (23 June 2009) Added a second metric auto loader to the Display
Control's Metric Settings page.
- (22 June 2009) Add text to the "out of memory" message that
indicates non-English character sets may be the cause of the problem.
- (18 June 2009) Made fixes to landmark vector surface-based
registration algorithm.
- (18 June 2009) Print an error message if a named matrix does not
exist when "caret_command -surface-apply-transformation-matrix" is run.
- (15 June 2009) Added dilation mode of metric smoothing.
- (15 June 2009) Updates and fixes made to the Surface Deformation
Dialog.
- (12 June 2009) Added "caret_command -surface-border-to-metric"
command that transfers the border's variance to nodes used by the
border.
- (12 June 2009) Modified Spherical Deformation Dialog for the
spherical vector algorithm.
- (27 May 2009) Fixed export of Free Surfer Label files from caret5.
- (19 May 2009) Fixed crash that occurred when trying to smooth a
spherical surface using the GUI.
- (13 May 2009) For coordinate difference, allow the XYZ component
differences to be absolute value or signed.
- (08 May 2009) Report crossovers during any cycle of spherical
deformation. Save source and target borders at beginning of each
cycle.
- (08 May 2009) Add previous directories list to the file dialog
for selecting a deformation map file on the spherical deformation
dialog.
- (08 May 2009) Change the surface deformation dialog so that it is
non-modal.
- (07 May 2009) Display Control:Surface Miscellaneous Page:Link
Size now affects "Links (No Backside) drawing mode.
- (28 April 2009) Fixed bug that caused border line width to affect
the link size in surface links no backside drawing.
- (28 April 2009) Add names of deformation map files to Deformation
page of Flat/Spherical Deformation Dialog.
- (27 April 2009) When running spherical deformation through the
GUI and there is a surface in the main window at the time deformation
is run, see that any surface displayed during spherical deformation are
displayed in the same orientation as the surface that was originally in
the main window.
- (10 April 2009) Correct writing of NIFTI volume QFORM information
so that QFORM is correct when read by programs that choose QFORM over
SFORM.
- (10 April 2009) Modified the Apply Current View code so that it
no longer uses OpenGL subroutines for matrix computations. As a
result, the compressed medial wall surface can now be generated on the
command line.
- (08 April 2009) For "caret_command -surface-generate-inflated",
disable the compressed medial wall option since it will not work on the
command line due to its usage of an OpenGL method for rotation.
- (03 April 2009) Fixed display of foci linked to table with a
blank table subheader.
- (01 April 2009) Fixed a crash caused by two nodes have an
identical coordinate during surface morphing. Also, tests for NaN
where added if debugging is on.
- (30 Mar 2009) Fixed problem with reading GIFTI data files that
caused the file's metadata to be missing. This problem was
discovered when foci were not projecting due to the surface's structure
being invalid.
- (04 Feb 2009) Fixed crash that occurred if the last column of a
node attribute file was deleted using the Manage Loaded Files Dialog.
- (29 Jan 2009) Changed version
to 5.611.
- (29 Jan 2009) Removed the "8081" sums host from the SumsDB dialog.
- (27 Jan 2009) Fix excessive pop-ups of the L-to-L, R-to-R warning
such as when scenes are displayed.
- (27 Jan 2009) Modify foci study validation to check that a focus'
class name matches either the linked table subheader short name, figure
panel task description, or page reference subheader short name.
- (27 Jan 2009) Added "caret_command
-surface-foci-reassign-study-names" to set foci names to study names.
- (09 Jan 2009) Add an option to the Surface Region of Interest
Dialog that allows limiting the ROI to a three-dimensional region.
- (09 Jan 2009) Add message that pops up when a "Left-toLeft,
Right-to-Right" selection is made on the display control.
- (09 Jan 2009) Added "caret_command
-surface-border-set-variability".
- (16 Dec 2008) Add foci color list id to study collection file.
- (15 Dec 2008) Changed "caret_command -deformation-map-apply" by
replacing METRIC with METRIC_AVERAGE_TILE and METRIC_NEAREST_NODE.
- (10 Dec 2008) Fixed bug that caused caret_command to always turn
off the debug settings in the preferences file.
- (07 Dec 2008) Add the foci SuMS items to the foci report.
- (05 Dec 2008) Add "caret_command -study-metadata-file-validate"
to validate the contents of a study metadata file.
- (04 Dec 2008) Add "caret_command -surface-foci-study-validate" to
find problems with foci linking to studies.
- (04 Dec 2008) When writing a foci file in CSV format, insert a
space at the beginning of the area field if the area field begins with
a number. Otherwise, Excel will convert something like "9/6" into
"6-Sep" and hose everything up.
- (25 Nov 2008) Remove "Page Number" from Study Metadata Link
Dialog. Ignore "Page Number" listed in any foci, foci projection,
or study metadata link files. "Page Number" conflicts with the
"Page Reference" that may be associated with a study.
- (24 Nov 2008) Added "caret_command
-surface-roi-node-areas". Also added a page the Surface ROI
Dialog to compute node areas.
- (19 Nov 2008) Changed version
to 5.610.
- (19 Nov 2008) For Surface->Measurements->Generate Distance
Surface A to Surface B, do not allow selection of column and
automatically create the dx, dy, and dz columns.
- (14 Nov 2008) Disable "Fetch from PubMed" button on Study
Metadata Editor if there are no studies.
Release Version 5.61 (12 Nov 2008)
- (12 Nov 2008) Added Study Page Reference Page Number and Study
Page Reference Subheader to the Foci Report.
- (12 Nov 2008) Added Study Page Reference Page Number and Study
Page Reference Subheader to the CSV Foci File Format.
- (12 Nov 2008) Modify setting of class name with Table Subheader
Short Name to also use Figure Panel Description and Page Reference
Subheader Short Name.
- (11 Nov 2008) Add "caret_command -surface-distortion".
- (10 Nov 2008) Verify structure in each of the input cooridnate
files used by the landmark identification algorithm.
- (10 Nov 2008) Added study collection ID to study collection
editor.
- (10 Nov 2008) Added a button to the study metadata editor that
allows selection of a study by the study's name.
- (10 Nov 2008) Added FociList_ID to study collection file and
reorder items listed on study collection editor.
- (10 Nov 2008) In foci report, provide additional information if
there are mismatched foci in a foci report.
- (06 Nov 2008) Fixed writing of FreeSurfer Functional Data Files.
- (03 Nov 2008) Fixed creation of new Study Collection so that the
studies are the correct "x" studies and not the first "x" studies.
- (03 Nov 2008) "caret_command -color-file-create-missing-colors"
now accepts border, cell, or foci files.
- (03 Nov 2008) Added foci counts to Foci Attribute Report.
- (03 Nov 2008) Fixed ROI Text Report so that it shows the correct
coordinate file name.
- (28 Oct 2008) In Foci Report, change "Study Name" label to "Study
Title" since it actually displays the title.
- (28 Oct 2008) Fix label on Display Control Scene Page "Itentity"
to "Identify".
- (28 Oct 2008) Add ZIP file filter for SuMS Dialog's upload files
selection.
- (28 Oct 2008) In Foci Report, always show PubMed ID, even if it
does not link to a study. Report foci whose name does not match a
study name and PubMed ID's that do not match a study.
- (14 Oct 2008) Correct processing of arguments for brainfish and
gaussian algorithms with "caret_command -volume-map-to-surface".
- (13 Oct 2008) Fixed foci search when matching is none-of and the
attribute is empty. Changed label on dialog for entering foci
spatial search.
- (10 Oct 2008) When adding a new foci search set, allow user to
choose location of where the new foci search set is inserted within the
existing search sets.
- (09 Oct 2008) Allow foci density to be computed in density per
cubic centimeter in addition to the current density per cubic
millimeter.
- (07 Oct 2008) Catch all errors during "caret_command -show-scene".
- (07 Oct 2008) Fixed display of Label and File Button for Variable
List parameters in Caret Command GUI.
- (07 Oct 2008) Fixed scene display. If the previous scene
used an L-to-L R-to-R, the new scene did not display correctly.
- (07 Oct 2008) Add Species to Foci Search.
- (06 Oct 2008) Fix separation of study metadata file keywords that
are separated by "*"or "|".
- (03 Oct 2008) Add "caret_command -surface-folding-measures".
- (03 Oct 2008) Fixed bug with default parameters for command
"caret_command -volume-histogram".
- (03 Oct 2008) Add optional computation of the volume displaced by
a surface to "caret_command -surface-information".
- (03 Oct 2008) Allow editing of report in Surface Region of
Interest Dialog.
- (03 Oct 2008) Fixed bug in Surface ROI Paint Statistical Report
that occurred if a paint region contained no nodes in the ROI.
- (03 Oct 2008) Add previous directories to history section at top
of Text File Editor's Open and Save File Dialogs.
- (02 Oct 2008) Modify Volume Resizing Dialog so that it updates
the cropping slices after the Apply button is pressed.
- (01 Oct 2008) May have fixed crash during scene correction when
there was not a foci search page resulting from 22 Sep 2008 save
selected foci search to scene change.
- (30 Sep 2008) Add "-add-files-in-directory" option to
"-spec-file-create" that examines all files in the current directory to
see if they are Caret data files using the file name's extension.
If the file is recognized as a Caret data file, it is added to the spec
file.
- (29 Sep 2008) Changed way classes static variables are
initialized in the caret_files directory. This fixes an error
where the linker was unable to locate a static variables from a class.
- (23 Sep 2008) When reading a NIFTI volume file, allow sform_code
to have precedence over qform_code.
- (23 Sep 2008) Add Foci Attribute Report to Layers->Foci menu.
- (23 Sep 2008) List number of studies from which matching foci
originate on the Display Control's Foci Search page.
- (23 Sep 2008) Corrected foci search attribute display when loaded
from a Foci Search File.
- (22 Sep 2008) Save selected Foci Search in the Scene.
- (22 Sep 2008) Fix Delete Foci Not Displayed Due to Display
Control Selection so that it functions if a cerebellum is in the Main
Window.
- (22 Sep 2008) Foci Report: Add option for only displayed
foci. Add All On, All Off, and Core On buttons to foci attributes
section. Add All On and All Off buttons to paint attributes
section. Add scroll bars to entire dialog.
- (19 Sep 2008) Fixed problem reading an NIFTI volume that had
qform set, but not sform set, and units other than millimeters.
- (19 Sep 2008) Add "Attribute ID" to cells/foci.
- (19 Sep 2008) Add assignment of AttributeID to "caret_command
-surface-foci-attribute-assignment" and to Layers Menu->Attribute
Assignement.
- (18 Sep 2008) If a topology file is loaded due to it being
specified in a coordinate file header, add the topology file to the
spec file.
- (18 Sep 2008) Variable Value's in Script Builder now have a
button which pops up a file dialog for easy file selection.
- (17 Sep 2008) Fixed crash that occurred if a spec file was loaded
that contained coordinate files but no topology files.
- (17 Sep 2008) Do not print message about CARET_DEBUG when caret
is started.
- (17 Sep 2008) Fixed bug that occurred when reading foci files in
CSV file format. Trolltech's QFile::peek() appears to now read
one less character than requested.
- (16 Sep 2008) When generating a cerebral hull volume, add 7
slices around all faces to prevent the dilation from hitting the edge
of the volume file.
- (16 Sep 2008) Added stereotaxic space to cell/foci report.
- (16 Sep 2008) Fixed display of Areal Estimation Color Key.
- (16 Sep 2008) Fixed selection of areal estimation column on
Display Control's Areal Estimation page.
- (16 Sep 2008) Added species to study metadata.
- (09 Sep 2008) Add new full hemisphere flattening to Surface Menu.
- (09 Sep 2008) Fixed Segmentation Volume Topology Report which was
reporting an incorrect number of objects.
- (08 Sep 2008) When applying cuts, also remove islands from the
surface.
- (05 Sep 2008) Add generation of compressed medial wall so surface
generation process.
- (04 Sep 2008) Fixed various compilation warnings that occur on
Linux, typically "no newline at end of file".
- (04 Sep 2008) Fixed problem with execution of a caret script when
a comment contained a variable name prior to defining the value for the
variable.
- (04 Sep 2008) Add Study PMID to focus report.
- (04 Sep 2008) Make all file filters available for GUI to add to
spec file command line command.
- (04 Sep 2008) Fixed problem with the variable list parameter of
the Caret Command GUI when there was only a newline separating some
text.
- (03 Sep 2008) Modified algorithm that generates sulcal
identification that is used in automatic flatten and registration
landmark generation. Specifically, the depth tolerance for the
hippocampal fissure (SUL.HF) was too low which resulted in no
hippocampal fissure being identified. An iterative process has
been added that gradually reduces the depth tolerance so that the
hippocampal fissure is identified.
- (03 Sep 2008) If landmark border drawing of a segment from dorsal
part of hippocamapl fissure to the poster part of the corpus callosum
while following negative curvature fails, draw using the geodesic
method event though border may be incorrect.
- (03 Sep 2008) Added new structures, "all", "cerebrum_cerebellum",
and "subcortical".
- (03 Sep 2008) Add "caret_command -surface-foci-projection-pals"
which projects foci to the PALS atlas.
- (02 Sep 2008) Only allow selection of transformation axes in the
main window.
- (02 Sep 2008) Add volume cells and transformation cell files to
the cell color key.
- (29 Aug 2008) Fixed Caret Script/Command problems involving
parameters enclosed in double quotes containing blank characters.
- (29 Aug 2008) Fixed problems with cell/foci attribute assignment
when not all surfaces are provided.
- (29 Aug 2008) When reading foci from a CSV format file, always
create a study meta data link.
- (28 Aug 2008) Add creation of flattening and registration
landmark borders to Border Operations Dialog.
- (28 Aug 2008) When using "caret_command
-surface-foci-attribute-assignment" allow the user to specify NONE for
the coordinate and topology file of a surface that is not to be used
for attribute assignment.
- (27 Aug 2008) Added button to Color Key Dialog that clears the
highlighting.
- (27 Aug 2008) Added "caret_command
-surface-border-create-average" which creates an average border file
from two or more border files.
- (26 Aug 2008) Added "Caret User's Email Archive" which displays
the archive of postings to the caret-users email list.
- (25 Aug 2008) Added categoryID to Study Collections.
- (25 Aug 2008) Fixed operation of Close button on SumsDB Dialog.
- (25 Aug 2008) Fixed login to Sums that broke as a result of
recent QT library update. Used to get "set-cookie" now get
"Set-Cookie".
- (25 Aug 2008) Added Study Table Number, Study Table Subheader,
Study Figure Number, Study Figure Panel, Study Page Number to Foci
Report.
- (22 Aug 2008) Added mslID, parentID, coreDataCompleted,
completed, and publicAccess to StudyMetaData. Add entries on
Study Metadata Editor but do not let users alter the values.
- (21 Aug 2008) Update QT GUI libraries to 4.4.1.
- (20 Aug 2008) Removed "Shell Command Window" from Window Menu.
- (20 Aug 2008) Removed SuMS Tutoria and Altas menu items for the
Help Menu.
- (20 Aug 2008) Removed "Surface Menu->Geometry Menu->Nearest
Spherical Border Distance" menu item.
- (20 Aug 2008) Removed "Clear All or Part of XXX File" from
Attributes Menu-> Areal Estimation, Lat/Long, Metric, Paint,
and Surface Shape menus. These functionalities are now available
on the File Menu->Manage Loaded Files.
- (20 Aug 2008) Removed "Compute Average Separation Between Border
Points" from Layers->Borders Menu.
- (20 Aug 2008) Fixed bug that failed to set the algorithm for
"caret_command -volume-map-to-surface-pals".
- (20 Aug 2008) Replace Surface->Project to Plane Menu with a
dialog. Also add projection options for X and Y planes.
- (19 Aug 2008) Added "caret_command
-surface-foci-attribute-assignment" which is the command line
equivalent of Layers Menu->Foci->Attribute Assignment.
- (18 Aug 2008) Add "Update Focus' Class Name With Table Subheader
Short Names" to the Layers Foci Menu. If a focus is linked to a
table subheader, the focus' class name is replaced with the short name
from the table subheader.
- (15 Aug 2008) Added "caret_command_test -volume-topology-report"
to report topological information about segmentation volume files.
- (15 Aug 2008) On Volume Menu->Segmentation->Reconstruct
Into Surface Dialog, if hypersmooth surface is requested, generate an
inflated surface.
- (15 Aug 2008) Allow mapping to RAW surface when mapping volumes
to surfaces.
- (14 Aug 2008) Removed old Surface Region of Interest item from
Surface Menu.
- (11 Aug 2008) Removed Study Meta-analysis file.
- (08 Aug 2008) Add yoking to scenes.
- (08 Aug 2008) Fixed Display Control bug that caused the node ID
symbols to become black when the Surface Miscellaneous page was
displayed.
- (08 Aug 2008) Fixed bug that failed to set the scene files
modification status when a scene was replaced.
- (08 Aug 2008) Made corrections to volume to surface mapping's
interpolated voxel algorithm.
- (07 Aug 2008) Fixed problems with some of the volume to surface
mapping algorithms that were not using the "voxel box size" correctly.
- (05 Aug 2008) Added StudyCollectionFile for use by WebCaret.
- (05 Aug 2008) Add transformation matrix to loaded file management
dialog.
- (05 Aug 2008) Fixed use of Neighbor Box Size when mapping volume
to surface that broke during the 29 July voxel center revision.
- (05 Aug 2008) Add new RGB Paint Selection Page to Display Control
Dialog.
- (04 Aug 2008) When reading a file's header, convert the
"hem_flag" tag to "structure". This problem was noticed when
trying to project foci to the PALS atlas.
- (04 Aug 2008) Enable Overlay in "Coloration Applies To" on
Display Control's RGB Paint page.
- (30 July 2008) Added GIFTI Time Series File to the Open Data File
Dialog's list of file types.
- (29 July 2008) Revised volume
processing so that the origin and any coordinates are at the CENTER of
the voxel.
- (29 July 2008) Fixed possible segmentation glitch. Prior to
segmentation, an extra slice (padding) is added around all six faces of
the volume. If any of the face slices of the volume contained
non-zero voxels prior to padding, these non-zero voxels were added to
the padding.
- (28 July 2008) Installed new MINC and NETCDF libraries on the Mac
OSX version of Caret in order to fix reading of MINC volumes on Mac
Intel computers.
- (25 July 2008) Add new coloring mode that blends the colors of
the three overlays. It is selected near the bottom of the Display
Control's Overlay/Underlay Surface page.
- (25 July 2008) Fixed preservation of color and cell/foci
filenames when data read from comma separated value files.
- (25 July 2008) Fixed some missing file type labels on Manage
Loaded Files Dialog.
- (24 July 2008) Add Sums Color ID to ColorFile. Add SuMS
Version Number and SuMS MSLID to foci/foci projection files.
- (24 July 2008) Add Donna's modification for non-human species to
SureFit Segmentation algorithm.
- (24 July 2008) Changed how Caret handles stereotaxic spaces and
species since these values are critical for operations such as
segementation and automatic landmark border generation.
- (23 July 2008) Fixed bug that caused Caret to hang when
displaying oblique volumes and the Display Control's Volume Settings
page.
- (22 July 2008) Transformation Matrix Editor Window - Fixed crash
that occurred when creating a new matrix initialized to the Main Window
Surface transformation.
- (21 July 2008) Added "caret_command -image-format-convert" to
convert images to different formats.
- (21 July 2008) Fixed a bug that prevented the name of a volume
file from being reported if there was an error reading volumetric data.
- (17 July 2008) Added "Generate Colors for Paints without Colors"
to Volume->Paint menu to generate colors for volume region (paint)
names without corresponding area colors.
- (15 July 2008) When identifying nodes, both the nearest node and
the nearest tile under the cursor are selected. If both a node
and tile are identified, use a node from the tile if the tile is nearer
the viewer than the identified node.
- (15 July 2008) Manage Loaded Files Dialog now has a button for
saving all files detected as modified and also updates the spec file.
- (15 July 2008) Allow deletion of transformation data files
through the Manage Loaded Files Dialog. Set structure when cell
transform data files have a matrix applied so that they become surface
cells.
- (14 July 2008) Added a preliminary automatic landmark borders to
the SureFit segmentation algorithm.
- (14 July 2008) Fixed default naming of volume files.
- (14 July 2008) Use CTRL-M as a shortcut to launch the "Manage
Loaded Files" dialog.
- (11 July 2008) Fixed writing of RGB volumes.
- (11 July 2008) Corrected drawing
of volumes slices. The volumes slices are now drawn by placing
the voxel's coordinate in the center of the voxel. Previously,
voxels were draw as if the coordinate was at the corner of the voxel.
- (10 July 2008) Added "caret_command -image-to-web-page" that
assembles a set of images into one or a set of web pages.
- (09 July 2008) Corrected problem with Display Control's
Topography page selection of Eccentricity and Polar Angle.
- (09 July 2008) Fixed crash when deforming a topography file.
- (09 July 2008) Fixed setting of source and target directories on
Apply Deformation Map Dialog.
- (09 July 2008) Fixed problems with saving histogram as an image.
- (09 July 2008) Fixed problem with not mapping surface selected
when mapping volume to surface and using map to caret surface with
atlas with only Average Fiducial Mapping selected.
- (09 July 2008) When generating inflated, very-inflated, etc. from
fiducial, use the fiducial surface that is in the main window instead
of the "active" fiducial surface.
- (09 July 2008) When automatically aligning a surface after
multi-resolution morphing, add the name of the border projection and
the bordedr projection file to the coordinate file's comment.
- (08 July 2008) Added Tim's surface affine registration command.
- (08 July 2008) Add previous data file directories to open and
save data file dialogs.
- (03 July 2008) Add opacity to the surface. Opacity is
controlled on the Display Control's Surface Miscellaneous page.
Draw VTK models prior to drawing the surface so that the VTK model can
be seen when the surface opacity is lowered to allow
transparency. Otherwise the Z-buffer prevents one from seeing VTK
models that are within the surface model.
- (03 July 2008) Fixed resizing of main window when displaying a
scene with Window Positioning set to Use All Window Positions From
Scene.
- (03 July 2008) Fixed update of metric scaling column combo box on
Display Control's Metric Settings page.
- (02 July 2008) Now version
5.601.
- (02 July 2008) Add NIFTI GZIP as a volume type for segmentation.
- (02 July 2008) Write PNG images as compressed when capturing an
image and saving to an image file.
- (01 July 2008) Add TIFF for writing of images. TIFF
provides a lossless compression scheme (small file with no reduction in
quality).
- (30 June 2008) Add "-RANDOMSEED" option to all caret_command
operations so that the random seed can be set for statistical
operations.
- (30 June 2008) File Open Dialog - If both a paint and area color
files are selected for reading, read the color file first so that a
message stating "no area colors" loaded is not displayed. Perform
similar prioritizing for other color files and study metadata.
- (30 June 2008) Add /Volumes to File Dialog. Do not allow
consecutive duplicate entries in directory history combo box.
- (30 June 2008) After cleaning up paint names, update the GUI.
- (10 June 2008) Fixed path for caret_command when used by Command
Executor.
Release Version 5.6 (09 June 2008)
- (09 June 2008) Fixed Help Menu->Go To SuMS Database menu item.
- (09 June 2008) Updated WU IFH file now that its header file
contains the byte order. Previously, all IFH volumes were big
endian.
- (29 May 2008) Version 5.6
- (29 May 2008) Enable the
writing of GIFTI formatted data files. GIFTI is a standard
file format for the exchange of surface-based neuroimaging data.
It was created by the developers of AFNI/SUMS, BrainVisa, BrainVoyager,
Caret, CRkit, FreeSurfer, and VisTrails. Caret is able to read
and write GIFTI format coordinate, functional, label, shape, surface,
and topology files. For more information visit
http://www.nitrc.org/gifti.
- (29 May 2008) Corrected problem with Create Spec File Dialog not
using the correct directory.
- (28 May 2008) Add SuMS ID number, repeat number and parent cell
base ID to Cells, Foci, Cells/Foci Projections for use by SuMS.
- (28 May 2008) View Current
Files (on the File Menu) is now Loaded
File Management. Not only can the user view and delete files in
memory, but the user can also remove columns from node attributes files
and also check the modification status of files and save the files.
- (23 May 2008) Added "caret_command -image-resize" to resize
images including settings the resolution (dots per inch/meter).
- (22 May 2008) Add a search coordinate to each focus. When
foci have been projected to the PALS atlas, the foci may be in several
stereotaxic spaces. So, during projection to the PALS atlas, a
focus' search coordinate is always set to the position of the focus on
a FLIRT surface. During normal foci projection (to a surface, not
PALS), the search coordinate is set to the projected position.
Remove spatial search surfaces from the Foci Search page on the Display
Control.
- (20 May 2008) Added "caret_command -volume-map-to-vtk-model"
which maps a functional volume to a VTK surface model file.
- (19 May 2008) Do not perform surface identify operations when
surface viewing mode is hidden.
- (19 May 2008) Fixed recent bug in caret_command that prevented
locating the caret home directory.
- (16 May 2008) Make the default size of the caret command executor
dialog larger.
- (16 May 2008) Added "caret_command -scene-create" which is used
to create scene files on the command line.
- (16 May 2008) Added "caret_command
-surface-register-prepare-slits". This command is used prior to
spherical registration when an interspecies registration is performed
and there are functional areas not present in one species that are
present in the other.
- (15 May 2008) Add "Layers->Borders->Duplicate Border By
Name" that makes a copy of a border with a new name.
- (14 May 2008) Fixed problem with "Links (No Backside)" drawing
mode.
- (12 May 2008) Added "caret_command -surface-border-cutter" which
cuts surfaces using border projections.
- (12 May 2008) Added a new drawing mode "Tiles With Lighting No
Backfacing Tiles". With this drawing mode, the backsides of tiles
are not drawn which makes missing tiles appear as holes in the surface.
- (07 May 2008) Add "-surface-inflate" to caret_command for
inflating surfaces.
- (05 May 2008) Added support for reading GIFTI data files that use
NIFTI_INTENT_NODE_INDEX that indicate the file contains data for only a
subset of nodes.
- (05 May 2008) Add support for multiple transformation matrices
with GIFTI NIFTI_INTENT_POINTSET (coordinate) data arrays.
- (01 May 2008) Fixed bug in metric clustering so that it ignores
disconnected nodes. This was found during one-way ANOVA testing.
- (01 May 2008) Fixed bug in statistical clustering. If a
metric file was used it would cause a crash.
- (01 May 2008) Disabled generation of "Sulci ID" paint column in
the SureFit algorithm.
- (01 May 2008) Added option to GUI and command line
multi-resolution morphing to align the resulting surface to standard
orientation. It requires a border projection that identifies the
central sulcus.
- (25 Apr 2008) Add the "-CHMOD <permissions>" parameter to
ALL caret_command operations. This allows the user to set the
permissions on all files written during the commands operations.
- (25 Apr 2008) Aded "caret_command -spec-file-directory-clean"
which finds files in the current directory, but that are not in the
spec file, and either deletes the files, moves the files, or lists the
files.
- (23 Apr 2008) When creating standard or analysis grid borders,
clear out any existing borders.
- (18 Apr 2008) Add "caret_command -spec-file-clean" which takes a
spec file name as an argument and removes all entries from the Spec
File for which the corresponding file does not exist.
- (15 April 2008) When writing paint, shape, and area color files
in the SureFit Segmentation Algorithm, give them the description
"Initial" rather than the default such as "paint_file_##".
- (14 April 2008) Rewrote class that runs external programs so that
it is consistent across platforms and can capture output.
- (09 Apr 2008) Fixed a bug in the volume to surface mapper that,
on occaision, displayed the error "No Volume Provided" when mapping a
volume that was stored in a file.
- (08 Apr 2008) Add the "-CHDIR <directory-name>" parameter
to ALL caret_command operations. When this parameter is
specified, caret_command will run in the specified directory. It
does not affect the current directory of the shell that runs
caret_command.
- (04 Apr 2008) When creating the analysis grid borders, only warn
if the surface is not flat. After creating the analysis grid
borders, turn border display on.
- (01 Apr 2008) Added "Caret Help (Online)" to the Help Menu.
This displays the very latest help information from the Caret
website. This help information may be for a version of Caret that
is newer than the version the user is running.
- (01 Apr 2008) Add "caret_command -file-subsitution" which finds
and replaces text in a file.
- (18 Mar 2008) Add an erase mode to the Draw Border Update
Dialog. This new mode is used to erase part of a border.
- (18 Mar 2008) Modify reading of CSV file so that it reads Unicode
instead of ASCII.
- (17 Mar 2008) Correct update of Foci Attribute Assignment when
paint files are loaded. Add Cerebellum surface selection to Foci
Attrribute Assignment Dialog.
- (17 Mar 2008) Eliminated warning about modified palette when
trying to create a new scene.
- (14 Mar 2008) Add "Short Name to Foci Class" button to Study
Table
Sub Header. If pressed any foci linked to this Sub Header have
their class changed to the Sub Header's Short Name.
- (12 Mar 2008) Added a button to create a new search by copying an
existing search to the Display Control's Foci Search page. Also
change the "Search Number" label to a button so that a search can be
selected by name.
- (11 Mar 2008) Default new Foci Search Categories to ALL.
- (11 Mar 2008) Fixed bug so that all vocabulary files are listed
on the View Current Files Dialog.
- (11 Mar 2008) Modified Display Control's Scene Page's Transfer
Identify Filters so that they may be transferred to the current
Identify Window.
- (11 Mar 2008) Corrected problem with initialization of Foci
Spatial Search Surfaces when the spec file is changed.
- (11 Mar 2008) Added a 2mm FLIRT stereotaxic space.
- (11 Mar 2008) Fixed a crash that occurred when a scene was
created after deleting all surfaces of a specific hemisphere.
- (11 Mar 2008) Fixed problem with cerebellum volume/surface
interaction.
- (10 Mar 2008) Correct origins for some 711* stereotaxic spaces.
- (07 Mar 2008) Added "caret_command
--surface-align-to-standard-orientation" which aligns a flat or
spherical surface to standard orientation.
- (07 Mar 2008) Fixed bug with flat surface alignment. It was
failing to translate the surface so that the ventral tip of the central
sulcus was at the origin.
- (06 Mar 2008) Added "caret_command_test -volume-file-merge" which
combines volumes representing left and right hemispheres into a single
volume file.
- (06 Mar 2008) Fixes for proper coloring of multiple probabilistic
atlas volumes or when changing probabilistic atlas volumes.
- (05 Mar 2008) Fixed display of cerebellum surface selection on
unproject foci to volume dialog.
- (03 Mar 2008) Add foci structure to ID window filtering.
- (03 Mar 2008) Add highlighting for probabilistic atlas color key.
- (03 Mar 2008) Do not report table metadata when focus color
selected on foci color key dialog.
- (03 Mar 2008) Add Cerebellum to
PALS atlas for functional mapping and stereotaxic foci projection.
- (03 Mar 2008) Controls have been added to the Display Control's
Surface Misc page that allows selection of the left, right, and
cerebellar surfaces used during surface and volume interaction.
- (27 Feb 2008) Add Draw Border Update to the Layers->Borders
Menu. This menu item allows the replacement of a segment in a
border
- (25 Feb 2008) Fixed display of RGB Paint data so that underlaying
data is displayed when RGB = (0, 0, 0).
- (22 Feb 2008) Add caret_command "-image-insert-text" and
"-image-combine".
- (22 Feb 2008) Change inputs to "caret_command -show scene" so
that user may choose how images of multiple windows are assembled.
- (22 Feb 2008) Fixed problem with Map Volume To Surfaces that
showed both Metric and Paint options when mapping to Caret Surfaces
with PALS atlas.
- (20 Feb 2008) Change "Layers->Foci->Delete Foci Not
Displayed on Main Window Surface" to "Delete Foci Not Displayed due to
Display Control Selections". It now deletes all foci that are not
displayed due to Display Control Selections with a possible popup to
also remove those not on the Main Window Surface.
- (20 Feb 2008) When identifying a focus, link Area, Geography, and
ROI to Vocabulary.
- (20 Feb 2008) Change foci attribute assignment dialog so that it
is non-modal and add an option to clear the attribute.
- (20 Feb 2008) Add Focus ROI to focus search.
- (20 Feb 2008) Add Focus ROI and Comment to Name Selection Dialog
data types.
- (20 Feb 2008) Fix highlighting of volume foci (foci are
highlighted by clicking the color bar in the foci color key).
- (19 Feb 2008) Add foci comment to foci search.
- (19 Feb 2008) Discovered that MNC volumes written on Microsoft
Windows cause the MNC API to abort when reading the file on a Apple
Macintosh with an Intel processor. This problem will not be
fixed. The solution is to write the volume in a different format,
such as NIFTI on Windows, and then transfer the file to a Macintosh.
- (18 Feb 2008) Add an interpolation method to volume resampling
(Edit Volume Attributes Dialog or caret_command) so that paint and
probabilistic volumes can be resampled.
- (18 Feb 2008) Surface Region of Interest Dialog: rearrange
selection page a little bit and set the style to modern style to reduce
size of dialog on Macs.
- (18 Feb 2008) Add "-surface-border-reverse" to caret_command to
reverse the order of links in a border.
- (15 Feb 2008) Fixed crash that occurred when toggling volume
probabilistic atlas areas.
- (14 Feb 2008) Changed "caret_command
-surface-sulcal-named-all-identification" so that it assumes volume
files listed in the input CSV file are located in the same directory as
the input CSV file.
- (14 Feb 2008) Add "Transfer Identity Window Filters" to the
Display Control's Scene page. Pressing this button allows the
user to choose a scene and then the Identity Window Filters are
transferred from this scene to all of the scenes selected on the
Display Control's scene page.
- (14 Feb 2008) Add Ontology Source and Term ID to Vocabulary.
- (13 Feb 2008) In the Identify Window, for PubMed ID, show only
the PubMed ID, not the full URL.
- (13 Feb 2008) When creating spec and scene files from selected
scenes, add proper filename extensions, if needed.
- (13 Feb 2008) Add Labels to foci search parameters. Add
Stereotaxic Space, Data Format, and Data Type to Foci Search.
Replace "Apply Search" button with "Search All" and "Search Displayed"
buttons.
- (13 Feb 2008) Added "-volume-prob-atlas-to-functional" and
"-volume-file-combine" to caret_command.
- (04 Feb 2008) Add region of interest category to foci.
- (04 Feb 2008) Add using the the image on the clipboard as the
captured image on the Image Capture Window.
- (01 Feb 2008) Fix problems with selection of a Selection File
column.
- (31 Jan 2008) Improved Image
Capture Window is compelete.
- (31 Jan 2008) Add additional windows to Capture Image of Image
window.
- (31 Jan 2008) Add capture of Main Window and all Open Viewing
Windows into a composite image to the Capture Image of Window Dialog.
- (30 Jan 2008) Add option to automatically crop the captured image
to the Capture Image of Window Dialog.
- (30 Jan 2008) Add option to modify the captured image's size on
Capture Image of Window Dialog.
- (30 Jan 2008) Removed Save As Image button from Display Control
since an image of the Display Control can be captured using the File
Menu->Save Window as Image Dialog.
- (30 Jan 2008) Update dialog for capturing Main Window images by
adding ability to capture image of Main Window, any Viewing Window, and
some of the common Dialog Windows.
- (30 Jan 2008) Replace Image Editor's Resize Dialog with one that
allows the user to set the size of the image in cm, inches, or mm and
the resolution of the image (pixels per cm/inch/mm).
- (30 Jan 2008) Fixed writing of multi-brick paint volumes which
requires synchronizing the region names of all of the volumes.
- (29 Jan 2008) Add border report options to caret_command's
"-surface-border-variability".
- (28 Jan 2008) On Display Control's Surface Shape Settings page,
default the color mapping column to the highest priority selected
surface shape column.
- (28 Jan 2008) Fixed reading and writing of Surface Vector Files
in binary format.
- (28 Jan 2008) Fixed selection of surface vector file data on the
Display Control Dialog.
- (28 Jan 2008) ZIP NIFTI volumes when compress checkbox is checked
on the Save Data File Dialog.
- (25 Jan 2008) Add Foci Density to Functional Volume to the
Layers->Foci menu.
- (25 Jan 2008) Fixed problem with slow drawing of functional
volumes.
- (25 Jan 2008) Added a button to the color editor for changing the
name of the selected color.
- (25 Jan 2008) Fixed file filter used when choosing a volume on
the surface to volume dialog.
- (25 Jan 2008) Changed foci uncertainty limits to RGB paint so
that nodes without nearby foci are assigned the color (-1, -1, -1)
which is the RGB Paint "clear" color that allows the underlay to show.
- (25 Jan 2008) Fixed problems with layout of RGB information in
the Identify Window.
- (24 Jan 2008) Added "Resize Viewing Windows" to the Windows
Menu. This allows the user to resize all of the viewing windows
so that the graphics area displaying the brain models is same size as
one of the viewing windows' or the Main Window's graphics area.
- (24 Jan 2008) Fixed crash of cell/foci report dialog that
occurred if a cell's study info index was invalid.
- (23 Jan 2008) Add "Unproject Foci to Volume" to the
Layers->Foci menu that unprojects foci to left and right surfaces in
order to set the volume coordinates for the foci.
- (23 Jan 2008) Eliminated volume
foci. Foci loaded as a foci or foci projection file will show up
on volume slices. This change was made so that all foci (either
on the surface or on volume slices) can be controlled and searched on
the Display Control Dialog.
- (23 Jan 2008) Add additional foci search options for Study
Authors, Study Name, and "ALL".
- (22 Jan 2008) When viewing windows 3-10 are opened, set their
size to the size of viewing window 2 if it is open.
- (22 Jan 2008) Fixed layout problem on Display Control's Foci
Search page that placed the spatial search surfaces at the bottom of
the page after a large amount of empty space.
- (22 Jan 2008) Fixed display of identification information for
volume foci.
- (22 Jan 2008) On data type selection pages, show the data types
in the model selection overlay control. When going to a data type
selection page, set the model overlay control to the highest priority
overlay that is set to the data type.
- (22 Jan 2008) Fixed mistaken appending of ".cell" when saving a
foci file.
- (22 Jan 2008) Correct display of foci without keywords or link to
a study.
- (22 Jan 2008) When adding new Subheaders to a Table or Page
Reference in the Study Metadata Editor, automatically initialize the
Subheaders number to the number of Subheaders in its parent Table or
Page Referrence.
- (18 Jan 2008) Added new Surface Region of Interest Dialog.
This fixes problems with the previous ROI dialog being too tall on some
low-resolution displays and allows the user to choose the coordinate
and topology files for node selection and operation.
- (18 Jan 2008) Added button to Study Meta Data Editor that deletes
all studies that are not linked by the following file types: Areal
Estimation, Cells, Deformation Field, Foci, Geodesic, Lat/Lon, Paint,
Rgb Paint, Surface Shape, Surface Vector, Topography, and Vocabulary.
- (17
Jan 2008) Fixed display of surface shape colorbar.
- (17
Jan 2008) Add Foci Density to Metric Conversion to the Layers->Foci
menu.
- (15
Jan 2008) Add a Foci Search page to the Display Control Dialog.
This page allows the user to search foci for various attributes and
display only those foci meeting the search criteria.
- (15
Jan 2008) Modify Display Control Dialog's popup menu so that overlays
and the underlay can be selected.
- (08
Jan 2008) Display border names and colors, cell classes and colors, and
foic colors, classes, names, keywords, and tables alphabetically on the
Display Control Dialog.
- (08
Jan 2008) When performing metric animation (on D/C metric misc page)
and debug is on, add a caption to each image identifying the image's
metric column.
- (07
Jan 2008) Fixed problem with using the context sensitive mouse for
identifying cellls, foci, and borders.
- (26
Dec 2007) Remove leading and trailing whitespace from study names and
foci names so that comparing the names functions correctly when
updating foci study links by matching foci names to study names.
- (26
Dec 2007) Upgrade to QT 4.3.3 on Linux and Windows.
- (24
Dec 2007) Added "-surface-roi-statistical-report" to
caret_command. This new operation runs a statistical report on
the nodes selected in a surface region of interest file.
- (20
Dec 2007) Added the list of drives to sidebar of the File Dialog.
- (19 Dec 2007) Added new Surface
Overlay System that make each overlay independent from the
others. As a result, this allows the use of a different data type
in multiple overlays. For example, three metric columns may be
displayed with each column in a different overlay. In addition,
there are now three overlays and one underlay.
- (19 Dec 2007) Fixed problem with updating study metadata links
for foci by matching the focus name to the study name. This
operation failed when a focus did not have any study metadata links.
- (18 Dec 2007) Fixed scene problem with probabilistic atlas
volumes.
- (13 Dec 2007) Added a "JPEG Image" movie mode to the Record Main
Window Images Dialog. The intent is to use a program such as
Apple's iMovie, Apple's QuickTime Pro, Adobe Premiere, or Microsoft's
Media Encoder to convert the JPEG image sequence into a movie.
- (13 Dec 2007) Added a button to the Viewing Window Toolbar
labeled "Swap". When pressed, the brain model in the viewing
window and the main window are swapped.
- (07 Dec 2007) Updated QT to 4.3.3 on Mac OSX.
- (06 Dec 2007) Added two search
capabilities to the Caret Help Window. The first search method
searches the loaded help page. The second search method searches
all help files.
- (06 Dec 2007) Fixed problem with metric animation interpolation
using an invalid index to get/set node coloring during color
interpolation.
- (05 Dec 2007) Add All On/All Off buttons to Identify Dialog's
Filter tab.
- (05 Dec 2007) Modifies reading of areal estimation files for
selective column loading. Added an Areal Estimation submenu to
the Attributes Menu that allows for clearing of Areal Estimation File
columns and moved the Generate Areal Estimation Map menu item to this
submenu.
- (05 Dec 2007) Fixes for recording on the Recording Dialog and the
Metric Settings Display Control page.
- (05 Dec 2007) Add control that sets the maximum distance a focus
may be from the surface to the Foci Attribute Assignment Dialog.
- (04 Dec 2007) Modified SureFit algorithms partial hemisphere
padding so that the padding receives a light amount of erosion.
Without this erosion, most nodes in the CUT.FACE region were removed by
the polygon simplification algorithm leaving many sliver triangles in
the surface.
- (03 Dec 2007) Add option to set the number of padding slices when
processing a partial hemisphere with the SureFit segmentation algorithm.
- (30 Nov 2007) Added import of MNI OBJ Polygon File.
- (30 Nov 2007) Finished removal of all QT3 Support code.
- (30 Nov 2007) Add Paint Name page to the Display Control
Dialog. This page allows selection of paint names for display.
- (29 Nov 2007) Fixed problem with padding of partial hemisphere
segmentations. The padding was using the last slice but should
have been using the second to last slice. See
http://brainmap.wustl.edu/pub/donna/ARCHIVE/BAD_LAST_SLICE/bad_last_slice.html.
- (29 Nov 2007) Removed mouse mode control (13 Nov 2007).
Modified the Toolbar View button so that it now contains a small
arrow. Pressing this arrow displays a menu for common mouse
modes. In addition, the context menu (right click on Linux and
Windows, CTRL-Click on Macs) display a mouse mode menu.
- (28 Nov 2007) Improved reading of NIFTI volumes that use QFORM
for orientation information but probably not totally correct.
- (28 Nov 2007) Fixed crash when File Menu->Set Current
Directory was used.
- (27 Nov 2007) Scenes changes now only retain surfaces and volumes
(except probabilistic volumes). An option for retaining foci,
foci colors, and study metadata has also been added.
- (26 Nov 2007) Changed version
to 5.512.
- (19 Nov 2007) Add "-volume-create",
"-volume-create-in-stereotaxic-space", and
"-surfaces-to-segmentation-volume-mask" to caret_command.
- (19 Nov 2007) On Save Data File Dialog, hide prob atlas volume
selection combobox so that all prob atlas volumes are saved to a file.
- (19 Nov 2007) Add StudyMetaDataLinks to Areal Estimation, Prob
Atlas Surface File, and Prob Atlas Volume File.
- (19 Nov 2007) Default the File Open Dialog to the current
directory.
- (19 Nov 2007) When a paint is identified, do not show linked
study metadata if the paint name begins with a question mark (?).
In addition do the same for metric values of zero.
- (19 Nov 2007) On Foci Attribute Assignment Dialog, allow
deselection of a hemisphere for assignment.
- (19 Nov 2007) Fixed display of foci geography attribute in
identification dialog.
- (16 Nov 2007) Add "-color-file-create-missing-colors" which adds
random colors to a color file for some data files when the data file
name does not have a matching color.
- (14 Nov 2007) Fixed bug with Surface Region of Interest Dialog,
which enabled the display of ROI nodes when displayed but failed to
check recheck the Show Selected Nodes checkbox.
- (14 Nov 2007) Fixed bug that prevented the Surface
Menu->View->Switch to User View menu from being loaded with saved
user views.
- (14 Nov 2007) Fixed bug that resulted in the a WuQFileDialog
always asking the user to confirm overwriting a file even if the file
did not exist.
- (13 Nov 2007) Add import of MDPlot and Neurolucida files to
caret_command -file-convert.
- (13 Nov 2007) Add mouse mode control to main window toolbar.
- (12 Nov 2007) Fix -cog option for caret_command
-surface-place-foci-at-limits.
- (12 Nov 2007) Add "Contour Information" to Layers->Contours
menu to show the geometric and section extent of the contours loaded in
Caret.
- (09 Nov 2007) Add a smoothing option to "caret_command
-surface-border-merge".
- (08 Nov 2007) caret_command -show-scene: Fixed problem with
transformations being incorrect for windows other than the main
window. This was due to the drawing always drawing in the
"main window" and using its transformation instead of the
transformation for the viewing window.
- (07 Nov 2007) Add multiple file writing preferences.
- (02 Nov 2007) Fix Display Control crash that occurred when a
paint column was selected on the Paint page prior to creation of the
Overlay/Underlay Surface page.
- (02 Nov 2007) Fix crash when choosing a directory on the Copy
Spec File Dialog.
- (02 Nov 2007) Fix very slow update of Display Control Dialog's
Shape Selection Page when loading additional surface shape file data.
- (02 Nov 2007) Fix reading of "Nearest Node" option on Border
Projection Dialog.
- (02 Nov 2007) Fix directory only mode on WuQFileDialog.
- (01 Nov 2007) Reformat preferences dialog.
- (01 Nov 2007) Remove speech generation.
- (31 Oct 2007) Add "-file-read-time" to caret_command to time the
reading of a spec file's data files and also some caret data files such
as coordinate, border projection, foci projection, metric, spec,
surface shape, and topology files.
- (31 Oct 2007) Modify file filters used on Open Data File Dialog
so that shape files can be opened as metric files and metric files can
be opened as shape files.
- (30 Oct 2007) Remove QT3 compatibility flag from qmake files so
that Caret no longer uses QT3 Support library.
- (30 Oct 2007) Added
multi-threaded spec file reading which can reduce the time to read a
spec file by 30% or more. To enable multi-threaded spec file
reading, go to the Preferences Dialog (on the File Menu for Linux and
Windows and Caret menu on Mac OSX) and set the File Reading Threads to
at least 2. A good setting may be 2 times the number of cores per
CPU times the number of CPUs.
- (24 Oct 2007) Add Study Data Type and Study Data Format to Study
Metadata.
- (23 Oct 2007) Fix appending of study meta data files so that
provenance data is not lost. When saving a study metadata file,
prompt for provenance data if there are any studies without provenance
data.
- (23 Oct 2007) Fix Layers-Border option on Display Control's
Overlay/Underlay Surface page.
- (22 Oct 2007) Add an option, "-allow-start-end-the-same",
to "caret_command -surface-border-draw-geodesic" that allows the output
border to contain only a single link.
- (22 Oct 2007) Added support for 64-bit signed and unsigned
integer data types for NIFTI volume files.
- (19 Oct 2007) Replace QFileDialog with WuQFileDialog, an improved
File Dialog.
- (19 Oct 2007) Fixed problems on Open Data File Dialog involving a
copy data file error and selection of file type when using the "any"
file filter.
- (19 Oct 2007) Fixed problems on Save Data File Dialog involving
incorrect file extension (.border) added to a border projection file
and not initializing the filter to the previous file filter.
- (19 Oct 2007) Fixed Sums Dialog's upload file dialog so that it
initializes to the current directory.
- (19 Oct 2007) Fixed prepending of column prefixes when deforming
node data files.
- (19 Oct 2007) Fixed update of column names on Shape Math Dialog
when the column names are changed on the Display Control Dialog.
- (17 Oct 2007) Add support for multiple Study Metadata Links.
- (12 Oct 2007) Add a command that finds duplicate studies in
StudyMetaDataFile's to caret_command.
- (09 Oct 2007) Add Open Inventor as one of the surface conversion
output formats for caret_command's "-file-convert".
- (08 Oct 2007) Combine Open Data
File, Import File, and Open Image
File Dialogs into a single dialog using a new and improved file
dialog. When opening files, multiple files may be selected.
- (08 Oct 2007) Combine Save Data
File, Export File, and Save Image
File Dialogs into a single dialog using a new and improved file dialog.
- (05 Oct 2007) caret_command updates: (1) add
"-deformation-map-create" to create a deformation map file from two
spherical coordinate files; (2) add conversion of caret shape file
column to a free surfer curvature file.
- (01 Oct 2007) Fixed bug that failed to display the Area attribute
on the Cell/Foci report dialog.
- (01 Oct 2007) Added "Attribute Assignment" to the Layers->Foci
menu that is used to assign the Area and Geography attributes of Foci.
- (28 Sep 2007) Fixed a bug that sometimes resulted in a node
attribute file (e.g. metric) having a blank column shown as selected on
the Display Control even though there is data loaded.
- (28 Sep 2007) Fixed problem with unicode characters in strings
returned by PubMed.
- (20 Sep 2007) Fixed cell density to metric operation crash that
occurred if the metric file contained one or more columns.
- (18 Sep 2007) Consolidate volume to surface metric and paint
mappers into a single mapper.
- (18 Sep 2007) Fixed bug, was using maximum voxel neighbors in
strongest voxel neighbors algorithm for volume to surface metric
mapping.
- (17 Sep 2007) Add backward and forward push buttons for page
selection.
- (17 Sep 2007) Added a variable input command to caret scripting.
- (13 Sep 2007) Added Provenance to StudyMetaData.
- (12 Sep 2007) Add "Generate Colors for Paints Without Colors" to
the Attribute Paint Menu. When selected, this will generate a
random color for any paint names that do not have a matching color with
the exact same name.
- (12 Sep 2007) Add new caret
script builder to the Window Menu.
- (07 Sep 2007) Fixed display of missing toolbar volume controls
when a volume in the 2nd or later brain set was selected for display.
- (04 Sep 2007) Change version to 5.511.
- (31 Aug 2007) Completed rewrite
of "caret_command". "caret_command" now includes the
functionality of the programs "caret_file_convert", "caret_copy_spec",
"caret_zip_spec", "caret_metric", and "caret_map_fmri". As a
result, these programs have been eliminated. Since
"caret_command" has been rewritten, the Script Builder Window,
available from the Window Menu, has also been eliminated since it is
incompatible. In place of it, for now, is "Caret Command
Executor", which provides a user-interface for executing all of
caret_command's operations. Since all of the metric/shape
statistical operations are in "caret_command", and Caret Command
Executor provides an interface to them, the Attributes Menu->Metric
and Shape statistical operations menu has been eliminated.
- (27 Aug 2007) Do not limit the size of foci. If being drawn
as OpenGL points do not allow the size to exceed the maximum
OpenGL allowed size.
- (27 Aug 2007) Add "Strongest Voxel" algorithm for mapping
functional volumes to surfaces. For each node, its value is the
value of the voxel that is furthest from zero in the local neighborhood.
- (23 Aug 2007) Allow cell/foci report dialog to function with both
left and right hemispheres.
- (10 Aug 2007) When "Update Focus PubMed ID if Focus Name Matches
Study" no longer clears the study link when the PubMed ID is not equal
to the Project ID.
- (31 July 2007) Fixed reading of gifti data arrays that had base64
encoding. Using "const QByteArray ba = text.toAscii(); and const
char* textChars = ba.constData();" instead of "const char* textChars =
text.toAscii().constData();" fixes the problem.
- (27 July 2007) Allow multiple spec files to be selected on the
Open Spec File Dialog. Multiple spec files are selected on the
dialog by using the CTRL or SHIFT keys and the mouse to select files.
- (24 July 2007) When caret is started with "-loadspec
spec-file-name" allow the entry of multiple spec files so that multiple
spec files my be loaded simultaneously.
- (19 July 2007) In Caret file name generation, ignore and no
longer use the date in the file name.
- (17 July 2007) Add buttons on Surface Region of Interest Dialog
for dilating and eroding the selected nodes.
- (17 July 2007) Modify automatic linear border drawing to generate
an error message if the starting and ending nodes in the border are not
connected in the region of interest.
- (16 July 2007) Fixed bug so that the color file symbol is
properly handled when appending a color file.
- (13 July 2007) Add buttons on the Surface Region of Interest
Dialog for saving or loading the current node selection.
- (06 July 2007) Fixed abort that occurred when creating a new spec
file on the spec file dialog.
- (05 July 2007) Display study information when a vocabulary entry
with a link to study metadata is identified.
- (05 July 2007) Correct reading/writing of study metadata links
for vocabulary files.
- (03 July 2007) At the beginning of surface flattening, check the
surface for topological errors (handles).
- (29 June 2007) If subject/species/hem not provided by spec file,
guess at their values by examining coord and topo file names.
- (29 June 2007) Add "-paint-composite" to caret_command.
- (22 June 2007) Add a full width half maximum algorithm to metric
smoothing. This algorithm smooths until the FWHM is achieved or
the maximum number of iterations is reached. The FWHM estimation
is based upon formula 2 of the Hagler et. al. article from NeuroImage
33 (2006) 1093-1103.
- (20 June 2007) Add a "1.0 - value" operation to volume and metric
math operations. The intended use is convert P-Values to
"Q-Values". If the users wants to threshold, say less than 0.05,
it cannot be done in Caret since caret thresholds "above" values.
So, using this operation will allow the user to threshold greater than
0.95.
- (19 June 2007) Remove all metric smoothing options except average
neighbors from the MetricFile. All algorithms remain in
BrainModelSurfaceMetricSmoothing.
- (19 June 2007) Add
multi-fiducial mapping of paint volumes to surfaces. These
options include mapping to the PALS atlas' individual cases, mapping to
the average fiducial surface, and in place of average to all cases a
most commonly mapped ID for each node.
- (19 June 2007) Fixed problem with paint "?" not properly enabled
on Display Control's Overlay/Underlay Surface page.
- (18 June 2007) When creating a new Study, have user enter the
PubMed ID if it is available. If the PubMed ID exists in another
study, do not allow the user to create a study using the same PubMed ID.
- (18 June 2007) Add provenance (submitter/originator) to Study
Meta Data File.
- (18 June 2007) Fixed parsing of caret data file names that
contained "LR" for the structure.
- (15 June 2007) Fixed reading of binary format latitude longitude
files.
- (14 June 2007) Add "-surface-to-cerebral-hull" to caret_command
for generating a cerebral hull volume from a fiducial surface.
- (13 June 2007) Add selection of nodes within a latitude/longitude
range on the Surface Region of Interest Dialog.
- (13 June 2007) Fix volume handle finder handle selection so that
it uses stereotaxic coordinates which will work when the underlay
volume is a different dimension than the segmentation volume.
- (12 June 2007 Add -metric-or-shape-stat-kruskal-wallis to
caret_command which performs a Kruskal-Walllis (non-parameteric one-way
ANOVA).
- (12 June 2007) Increase number of surface outlines shown over
volume slices and move the controls from Display Control's Volume
Settings page to a new page, Volume Surface Outline.
- (12 June 2007) Rebuild QWT libraries due to new QT libraries
installed on 08 June.
- (11 June 2007) Added a method to the foci projection file that
eliminates all foci not in a list of specified indices. This will
be used by WebCaret.
- (11 June 2007) Changed the following caret_command operations so
that they only the name prefix is specified for all output files:
"-metric-or-shape-stat-paired-t-test",
"-metric-or-shape-stat-one-sample-t-test",
"-metric-or-shape-stat-interhemispheric-clusters",
"-metric-or-shape-stat-anova-one-way",
"-metric-or-shape-stat-two-sample-t-test",
"-metric-or-shape-stat-coord-diff".
- (11 June 2007) Changed to version 5.510.
- (11 June 2007) Fixed cell/and foci reports so that they appear on
top
of the main window. They were, for some reason, appearing behind
the
main window.
- (08 June 2007) Switch to QT version 4.3.0. Gulp.
Release Caret 5.51 (07 June 2007)
- (07 June 2007) Changed version to 5.51.
- (06 June 2007) Added "-metric-or-shape-set-column-name" to
caret_comand which sets the name of a column.
- (06 June 2007) Added "-metric-or-shape-file-info" to caret_comand
which prints names and min/max values for all columns.
- (06 June 2007) Added "-metric-or-shape-set-column-to-value" to
caret_comand which sets all values in a column to a scalar value.
- (06 June 2007) Added "-metric-or-shape-create" to caret_comand
which creates a metric or shape file with specified number of nodes and
columns.
- (06 June 2007) Added "-metric-or-shape-correlation-map" to
caret_comand which creates a correlation map between two metric/shape
files.
- (05 June 2007) Added a page to www.wikipedia.org for CARET.
- (04 June 2007) Added keyboard commands for panning an zooming
contours.
- (30 May 2007) Modified algorithm that creates borders around
clusters so that it now creates borders around small clusters which it
did not do in the past. In addition, there is now an option to
automatically project the new borders and borders are automatically
displayed.
- (29 May 2007) Add Surface ROI option that creates a border from
an ROI that represent the fundus of a sulcus or crown of a gyrus.
- (24 May 2007) Fixed bug that borders were not displayed if they
were first enabled using the pop-up menu.
- (24 May 2007) Add option to Draw Borders Dialog that
automatically projects a border immediately after the border is drawn.
- (22 May 2007) Add -surface-roi-coord-report" to caret_command.
- (18 May 2007) Add ability to read free surfer patch files which
had their format changed in free surfer version 3.0.5.
- (17 May 2007) Add "-volume-histogram" to caret_command which
prints a histogram of the input volume to the terminal window.
- (17 May 2007) Add "-volume-scale-percent-min-max-255" to
caret_command which rescales voxel values excluding percentages
of the minimum and maximum values.
- (17 May 2007) Add "-volume-anatomy-peaks" to caret_command which
prints estimates of intensity values for CSF, gray, and white matter.
- (09 May 2007) When cropping a volume, save the cropping
parameters to the parameters file.
- (09 May 2007) Save gray and white peaks to the parameters file
when segmenting (it previously did this only for the GUI, not command
line).
- (07 May 2007) List the values of the estimated CSF, Gray, and
White peaks on the SureFit segmentation dialog.
- (07 May 2007) When reading a Neurolucida file, use "SID"
attribute of a contour's <point> as the section number.
- (04 May 2007) Remove use of vtkDecimateCaret and use
vtkDecimatePro instead.
- (03 May 2007) Fixed problem with ID node by number
(Surface->Identify menu item) not placing green ID symbols on
surface.
- (01 May 2007) At start of surface flattening algorithm, enable
the display of borders needed due to 26 April change.
- (30 April 2007) Add "Smooth" button to SureFit segmentation
dialog to smooth the histogram and help find gray/white peaks.
- (30 April 2007) Improved consistency of volumes so that
crosshairs are at the center of a voxel.
- (27 April 2007) Correct problem with foci name selections not
being saved to a scene.
- (26 April 2007) Default the display of borders OFF.
- (25 April 2007) Throw exception if reading a comma separated
value file is read and it is missing the "csvf-section-end" tag at the
end of the last data section.
- (25 April 2007) Fixed crash with View Current Files that occurred
if no surfaces were loaded.
- (24 April 2007) Make improvements in algortithm that estimates
the gray and white matter peaks in an anatomy volume.
- (23 April 2007) For statistical cluster finding algorithms,
generate a region of interest statistical report for each input/shape
file.
- (20 April 2007) For structure names allow a single character (L)
in addition to the full name (Left).
- (20 April 2007) When reading a foci file in CSV format, if the
structure is not specified, allow the sign of the X-coordinate to imply
the structure (minus implies left, positive implies right).
- (19 April 2007) Add left-to-left and right-to-right coloring
selections for paint and RGB paint.
- (19 April 2007) Add check to see if studies from a meta-analysis
already exist when working with Study Metadata.
- (19 April 2007) When importing data from a meta-analysis file,
allow appending or replacement of existing study metadata.
- (17 April 2007) Modify surface information reports so that the
surface extent is only for connected nodes.
- (17 April 2007) Add option "-vc" to caret_file_convert to convert
between volume file formats.
- (17 April 2007) Change version to 5.503.
- (17 April 2007) Add button to color selection dialogs that allows
selection of commonly named colors as defined by the world wide web
consortium.
- (16 April 2007) Added import of
MicroBrightfield's Neurolucida XML files that contain contours and
markers.
- (12 April 2007) Add a page to SureFit Segmentation Dialog that
allows the user to set the type of volume files that the segmentation
process will write.
- (10 April 2007) Added Bias
Correction of Anatomical Volumes. The algorithm was taken
from AFNI's program 3dUniformize.
- (10 April 2007) Added ID filtering of study meta-analysis
information on Identify Window.
- (09 April 2007) Add new meta-analysis file which contains one
meta-analysis study and a list of the studies contained in the
meta-analysis.
- (06 April 2007) When adding studies contained meta-analysis, make
retrieval of data from PubMed optional.
- (06 April 2007) Fix retrieval of Medical Subject Heading data
when retrieving Study Information from PubMed.
- (06 April 2007) Add a "link" button next to PubMed ID in study
editor to show the web page for the study.
- (06 April 2007) Show meta-analysis info for a study in the
Identify Window.
- (06 April 2007) Add ability to delete a group of studies by name
on the Study Metadata Editor dialog.
- (06 April 2007) Fix read of foci x-coord from a comma separated
value file.
- (06 April 2007) When study metadata editor dialog is launched and
there are no studies, create an empty study so that the dialog is
properly sized.
- (05 April 2007) Added option on
SureFit Segmentation Dialog to generate topologically correct
surfaces. This option is off by default. If turned on, a
dialog informs users about issues and limitation of this option.
- (05 April 2007) When generating a surface and maximum polygons is
selected, do not perform any polygon decimation. Previously, if
maximum polygons was selected, there was some polygon decimation
performed if it could be done with very minimal or not change in the
shape of the surface.
- (04 April 2007) Fix naming of surface shape files produced by
SureFit segmentation method so that the file name contains the number
of nodes.
- (04 April 2007) Add range of values to data type labels on volume
rescale dialog.
- (04 April 2007) Add -surface-information and
-surface-topology-disconnect-paint-nodes to caret_command.
- (03 April 2007) Add a PubMed ID to each Caret file. This ID
is entered on the File Menu->Save Data File Dialog.
- (02 April 2007) Add a Link button next to the DOI/URL on the
Study Metadata Editor. When pressed, it will use the DOI/URL to
show the article in a web browser.
- (02 April 2007) Add Meta-Analysis to Study Meta Data.
- (02 April 2007) Save cell/foci highlighting to scene..
- (29 Mar 2007) For Thesholding an Anatomical Volume into a
Segmentation Volume, an upper threshold was added, the thresholds are
now floats, and allowed to have a floating point values.
- (28 Mar 2007) Correct lighting problem with export to VRML files.
- (28 Mar 2007) Correct iterations problem with Paired T-Test.
- (26 Mar 2007) Enable reading of NIFTI volumes that are stored in
an analyze hdr/img file pair.
- (26 Mar 2007) Add option to pop-up menu to project the border
under the mouse.
- (23 Mar 2007) Changed reading of Caret data files in Comma
Separated Value File format so that the column names are case
insensitive.
- (22 Mar 2007) Added -volume-segment-mask-creation, which creates
a volume mask from a group of volumes, and -volume-mask-volume, which
applies a mask volume to a volume file, to caret_command.
- (22 Mar 2007) Added "Correct
Fiducial Surface Topology (Remove Handles)" to the Surface-Topology
menu. This operation will remove all topologial errors (handles)
in the main window fiducial surface. It does this by discarding
nodes around handles and retessellating the surface. While the
resulting surface is topologically correct it is not necessarily
anatomically correct.
- (22 Mar 2007) When drawing 3D borders, allow the mouse to rotate
the surface if the ALT key is depressed. This should help with
drawing flattening and registration borders as it will allow the
borders to be drawn on 3D (inflated, fiducial) surfaces instead of the
flat map and the compressed medial wall surface.
- (22 Mar 2007) Add selection of nodes that are crossovers to
surface region of interest dialog.
- (21 Mar 2007) Add "-surface-topology-neighbors" which generates a
list of neighbors for each node in a topology file.
- (20 Mar 2007) Fixed problem that occurred on some Linux
workstations with the Recording Dialog. On some Linux
workstations the function that reports if a file is writable always
returns unwritable.
- (19 Mar 2007) Add "Update Focus' PubMed ID if Focus Name Matches
Study Name" which updates the PubMed ID in the focus' study metadata
link if the focus name is the same as the name of a study.
- (19 Mar 2007) Add a "Fetch All PMIDs" button on the Study
Metadata Editor Dialog. This will update all studies with valid
PubMed IDs with data retrieved from www.pubmed.gov.
- (16 Mar 2007) When retrieving PubMed Info from the PubMed
website, append year, volume, and pages to journal name.
- (16 Mar 2007) Add Name and MESH (Medical Subject Headings) to
Study Metadata. Remove URL and combined it with DOI since DOI
should always go to the correct document.
- (15 Mar 2007) Implemented left-on-left, right-on-right coloring
option for surface probabilistic atlas.
- (14 Mar 2007) Added "Create Interpolated Borders" to the
Layers->Borders Menu. This allows the user to create new
borders that are interpolated between two selected borders.
- (13 Mar 2007) Add a "Fetch"
button in the PubMed ID row on the
Study Metadata Editor Dialog. When pressed, it grabs the
currently entered PubMed ID and queries the PubMed database for title,
author, citation, DOI, and abstract and places the results into the
currently edited study.
- (12 Mar 2007) Fixed problem with foci disappearing when old study
data was moved from the foci file to the study metadata file.
- (12 Mar 2007) Implemented the addition of a study metadata link
for volume files.
- (12 Mar 2007) Modify caret_command's two-sample T-Test to have an
option of using pooled or unpooled variance. Previously it always
did unpooled variance.
- (12 Mar 2007) Add "-volume-resize" to caret_command.
- (12 Mar 2007) Speed up shuffling of metric columns.
- (09 Mar 2007) Fix option on Volume Attributes Editor and Volume
Creation dialog for setting the attributes (dimension, spacing, and
origin) of a volume.
- (07 Mar 2007) For use with permuted metric/shape surface
statistics, add a metric file that shows the clusters. The metric
file contains two columns, the statistic and (1 - p-value). Use
(1- p-value) to threshold the clusters. A new palette
"plus_minus" was also added to assist with cluster display.
- (07 Mar 2007) Link to Study Metadata Dialog should now be
properly initialized when there is an existing link.
- (07 Mar 2007) Add information to the project cells/foci dialog
that informs user that the sign of the cell/focus is used to determine
the associated hemisphere.
- (06 Mar 2007) Add "Edit" buttons on spherical deformation dialog
that allow editing of the individual and atlas borders. This
allows the user to view the borders in a border file, change the names
of borders, and/or delete borders.
- (02 Mar 2007) Add one-way ANOVA
to caret_command. Using two input files, comparing the
results of a one-way ANOVA with a two-sample T-Test with pooled
variance results in the exact same clusters and the F-Statistics equal
to the square of the T-Statistic.
- (02 Mar 2007) Eliminated print statement "unknown paint file tag:
tag-version" message printed when reading a paint file.
- (01 Mar 2007) For foci identification in identify dialog and
filtering selection on the identify dialog change "Size" to "Extent".
- (01 Mar 2007) Fixed selection of a study on the link to study
metadata dialog. This is a QT issue as the signal cellChanged()
was no longer emitted so the signal was changed to cellClicked().
- (28 Feb 2007) Add "-metric-or-shape-copy-columns-to-new-file" to
caret_command. This new command creates a new metric file from
column copied from an existing metric file.
- (28 Feb 2007) Add metric/shape in group difference, which
computes the difference between all possible column combinations, to
caret_command. Use the "-metric-or-shape-in-group-diff" option.
- (27 Feb 2007) Fix use of optional inner and outer boundaries for
surface to volume conversion run with caret_command.
- (27 Feb 2007) Add buttons to Study Metadata Editor Dialog that
allows selection of studies by name or title.
- (27 Feb 2007) When deforming a coordinate file, preserve
structure, surface type, etc.
- (27 Feb 2007) Add entries on deformation and apply deformation
map dialogs to set the node data file deformed column name prefix.
- (27 Feb 2007) On apply deformation map dialog, add
"*.atlas.paint" to atlas file filter.
- (26 Feb 2007) Fixed scrolling of volume slice spin boxes when
holding down the mouse button.
- (26 Feb 2007) Fixed reading of NIFTI volume that required
rotation to become an LPI orientation.
- (26 Feb 2007) Add "Bring All to
Front" and "Stack Windows" to the Window Menu. "Bring All to
Front", available on Mac OSX only, places Caret's windows on top of
windows from any other applications. "Stack Window" places all
open dialogs/windows over the main window with a small offset.
- (23 Feb 2007) Add filtering for all remaining study metadata
items.
- (23 Feb 2007) When displaying a scene, assign colors to borders,
cells, and foci.
- (22 Feb 2007) Add filtering for study table data on Identify
Dialog.
- (22 Feb 2007) Add option on Display Control's Foci Page, "Show
Foci Pasted Onto 3D Surfaces" which "pastes" foci onto all 3D surfaces
to help expose subcortical foci.
- (22 Feb 2007) Correct Foci Color Key when foci are colored by
class name.
- (21 Feb 2007) When loading files through the spec file dialog and
if there are foci (or foci projection) files selected and there are
study metadata files but no study metadata files are selected, warn the
user. Also, list study metadata files when the foci filter button
is selected on the Spec File Dialog.
- (21 Feb 2007) When the name on a Foci Color Key is clicked, try
to find the corresponding study and display the study metadata in the
Identify Dialog.
- (21 Feb 2007) Automatically add a subheader when a new table is
created on the Study Metadata Editor Dialog.
- (20 Feb 2007) Add filtering of study information on the Identify
Dialog.
- (20 Feb 2007) Add filtering of foci information on the Identify
Dialog.
- (20 Feb 2007) Fixed uploading of files to SuMS Database.
This problem was a result of a bug that was supposed to have been fixed
in QT 4.2.2 (See 15 Feb 2007) but was not actually fixed.
- (15 Feb 2007) When reading cell/foci files and cell/foci
projection files, check for an invalid structure for a
cell/focus. If the structure is "invalid" set the structure to
"right" if the X-coordinate is greater than zero or set the structure
to "left" if the X-coordinate is less than zero.
- (15 Feb 2007) Some cell/foci files were not having their
structure read correctly but it seems to now be fixed as a result of
updating QT to QT 4.2.2. This problems was found when unit
testing of foci rendering failed.
- (15 Feb 2007) Added unit testing comparison for cell & foci
files.
- (14 Feb 2007) Updated QT to QT
4.2.2 since it is supposed to
contain fixes to bugs that I had reported. Unfortunately, not all
the bugs they claim to have fixed are corrected and they have added new
bugs such as a Q3FileDialog that is too large to fit on the
screen.
- (14 Feb 2007) Fixed crash that occurred when the current node
coloring was used to create a new rgb paint column.
- (12 Feb 2007) Corrected number of non-twin comparisons performed
in caret_command's -metric-or-shape-twin-comparison.
- (09 Feb 2007) Add options on the foci sub pages to display foci
without a class assignment, foci without a color assignment, foci
without a link to a study with keywords, and foci without a link to a
study table subheader.
- (09 Feb 2007) Change "Color" tab on D/C Foci page to "Name" since
foci colors are almost always the names of foci.
- (09 Feb 2007) Add option to assign the class name to all
displayed foci.
- (09 Feb 2007) Add option on D/C's Foci Main page to color foci by
focus name or by focus class name.
- (08 Feb 2007) Add display control of foci based upon the linked
study's keywords and table sub header names.
- (07 Feb 2007) Correct projection of foci to PALS atlas that broke
as a result of adding the new Study Metadata File.
- (02 Feb 2007) Fix cleanup paint names when there are multiples of
an identical name.
- (02 Feb 2007) Add deformation of cell/foci projection files.
- (02 Feb 2007) Move some stuff from the MathUtilities class to the
caret_statistics library.
- (01 Feb 2007) Add a new file, TextFile, for simpler reading and
writing of text files and comparison of text files.
- (01 Feb 2006) Enable metric/shape files to be read and written as
comma separated value files. Unfortunately, Microsoft Excel
(prior to Excel 2007) limits the number of rows to 65536.
OpenOffice Calc is also limited to 65536 rows.
- (31 Jan 2007) Fixed normalize distribution in a metric
file. Modified normalization algorithm so that it works with a
small number of values.
- (30 Jan 2007) Correct deformation of Foci files.
- (29 Jan 2007) Fixed deformation of probabilistic atlas files
(result of node attribute to gifti conversion).
- (29 Jan 2007) Fixed reading of StudyMetaData file's that
contained StudyMetaDataTableSubHeader elements.
StudyMetaDataTableSubHeader was replaced with StudyMetaDataSubHeader
when SubHeaders were added to pages.
- (29 Jan 2007) Corrected problem with provenance being updated for
all studies when a StudyMetaDataFile was both read and saved. The
modification status was triggered when tables and figures were read and
added to studies when the file was read.
- (29 Jan 2007) Fixed writing of Comma Separated Value File that
resulted in elements being enclosed in double quotes when they did not
need to be enclosed in double quotes.
- (26 Jan 2007) Add new implementation of Volume Region of Interest
Operations which adds a new "wizard" dialog, additional voxel selection
options, display of selected voxels, and additional operations on
selected voxels.
- (23 Jan 2007) Fixed P-Value generation for Levene's Test and
Metric T-Test, a result of 19 Jan change.
- (22 Jan 2007) Add "-metric-or-shape-twin-comparison" to
caret_command for use with twin subject comparisons.
- (19 Jan 2007) Rewrite and simplify some of the statistical code.
- (19 Jan 2007) Slow mouse speed for panning of contours in view
and alignment modes.
- (18 Jan 2007) Add generation of Root Mean Square (RMS) for metric
and shape files.
- (18 Jan 2007) Reorganize the basic statistics and move it to
caret_common/StatisticUtilities.h/cxx.
- (17 Jan 2007) Add item to Layers->Contours Menu to resample
all contours.
- (17 Jan 2007) Enable Transformation Matrix Editor to apply a
matrix to main window contours and contour cells.
- (16 Jan 2007) Print a count of the number of points in each
contour when reading a contour file. This is used to find
contours with an excessive number of points.
- (16 Jan 2007) Corrected identification text for voxels which was
mistakenly show the identification data more than once.
- (16 Jan 2007) The data type for study metadata table number,
subheader number, figure number, and page number were changed from
integer to string since they may contain non-numeric characters.
- (16 Jan 2007) Fixed scene bug that caused identified node symbols
to not be displayed. This was a result of new identification code
from 02 Jan 2007.
- (12 Jan 2007) Add "Page Reference" to Study Metadata File and
update Study Metadata editor.
- (11 Jan 2007) Rewrote the code that rotates a volume 90 degrees
clockwise about an axis looking from the positive end of the axis to
the negative end of the axis.
- (08 Jan 2007) Initial implementation of new Study Metadata File.
- (08 Jan 2007) When loading a spec file turn off node highlighting
(blue) cross.
- (02 Jan 2007) Redesign of
Identify Window. The window now
has tabs that show the identification text or a page that shows the
identification filtering selections. The filtering selections
were previously on the window's toolbar.
- (26 Dec 2006) Added volume yoking which is selected witht the
Yoke button on a Viewing Window Toolbar. When on, the selected
slices in the main window and the yoked viewing windows will be the
same anytime a selected slices is changed by using the slice controls
in the Toolbars or by identifying a voxel with the mouse.
- (22 Dec 2006) When reading a Comma Separated Value File (such as
one that contains foci), check for unicode's various dash codes
(em-dash, en-dash, etc. 0x2010 to 0x2015) and
underscores. If any are found convert them to minus signs.
In addition, print a warning message for any text to floating point
number conversions that fail.
- (15 Dec 2006) Fixed bug in surface areal smoothing that set a
node's XYZ coordinate to (0, 0, 0) if the node and its neighbors all
have the exact same XYZ coordinate. The smoothing algorithm uses
the area of triangles formed by a node and its neighbors and since the
nodes all have the same XYZ coordinate, the area of these triangles was
zero. The area of the triangles is used as a weight which results
in the weighted average of the neighbor's coordinates becoming (0, 0,
0). Since we use a smoothing strength of 1.0, a smoothed node's
new coordinates are entirely that of the neighbor's coordinates'
weighted average. The smoothing algorithm now performs no
smoothing of a node if the node and its neighbors all have the same XYZ
coordinate. In particular, this problem was noticed with
deforming a hull surface from one individual to another. It may
also be the cause of occaisional problems noticed in multi-resolution
morphing.
- (13 Dec 2006) Add one-sample T-Test, Paired T-Test, and
Interhemispheric Clusters to Statistical Algorithm Dialog.
- (12 Dec 2006) On statistical algorithm dialog, enabled running of
two-sample T-Test and Wilcoxon into Two-Sample T-Test operations.
Split surface files and cluster search parameters into separate pages.
- (12 Dec 2006) Add ability to run the metric/shape statistical
permutation algorithms (one-sample t-test, two-sample t-test, paired
t-test, etc.) using caret_command.
- (11 Dec 2006) Add distance and (x,y,z) components to output
metric file of the metric/surface shape t-map coordinate group
difference.
- (11 Dec 2006) Add opacity to border, cell, and foci display.
- (11 Dec 2006) Add a polygon reduction option to caret_command's
-volume-segment operation.
- (08 Dec 2006) Enable the cluster search used in the shape/metric
file statisical permuation algorithms to run as multiple threads in
order to reduce execution time.
- (08 Dec 2006) Modified SureFit segmentation algorithm so that it
may produce volume types other than AFNI (such as NIFTI).
- (06 Dec 2006) Allow a choice of symbols (OpenGL-points, squares,
boxes, rings, spheres, diamonds) for border drawing.
- (06 Dec 2006) Add "square" symbol for drawing foci. This is
similar to the existing point symbol, except that the square scales
with the size of the surface. This is unlike the Point symbol
(which is draw using OpenGL's GL_POINT) which remains fixed in size
even though the size of the surfaces changes.
- (06 Dec 2006) Add median and abs-median to Surface Region of
Interest Statistical Report.
- (06 Dec 2006) Fixed crash that occurred if Caret was unable to
open a file for writing.
- (05 Dec 2006) Fixed problem in segmentation automatic error
correction that prevented reporting of problems to the user due to an
improperlay handled exception.
- (04 Dec 2006) Fixed failure to display crossovers on initial flat
surface at the end of flattening.
- (01 Dec 2006) Add command line option "-notext" that disables
OpenGL text rendering. Some Linux systems have a problem with the
FreeType library that will cause Caret to crash.
- (01 Dec 2006) Change XML file identification to look for the
first ascii character that is not a space, tab, newline, or
linefeed. If this first ascii character is a '<' it will
assume the file is an XML file.
- (28 Nov 2006) Modify GuiBrainModelOpenGL to delete the memory for
BrainModelOpenGL when all windows are closed.
- (27 Nov 2006) Added "Integrated Folding Index" to the Surface
Region of Interest Dialog. Integrated Folding Index is for each
surface shape column and equal to SUM(Ai * Fi) / SUM(Ai) where Ai is
the area of a triangle and Fi is the average of the surface shape
value's for the triangle's three nodes.
- (22 Nov 2006) Added a new method named "crossover search" that
searches for topological defects in a segmentation volume. This
method operates by generating a spherical surface from the segmentation
volume, smoothes the spherical surface, and then checks for crossovers
in the spherical surface. Any crossovers are mapped into the
segmentation volume's space to an RGB volume and to the RGB paint file
on the surface.
- (20 Nov 2006) Added -surface-to-volume option to caret_command
for creating a volume from a metric/paint/shape surface file.
- (20 Nov 2006) Speed up mouse processing for contour alignment
translation on Linux and Windows.
- (20 Nov 2006) Fix contour set scaling when the scaling has
already been set.
- (17 Nov 2006) Bug fix to make checkable the Enable Rotation on
Volume->Transform menu item.
- (17 Nov 2006) Changes to OpenGL code for offscreen rendering.
- (16 Nov 2006) Added to the caret_command program:
-caret-data-file-compare which compares the data contents of two Caret
data files of the same type.
- (15 Nov 2006) Enable volume yoking so that a volume in the Main
Window may be yoked to a volume in one or more Viewing Windows.
Yoking is selected by using the Yoke button in the Viewing Window(s)
Toolbar.
- (15 Nov 2006) Add button to Toolbar in Viewing Windows, label
"UO" (Underlay Only), that is shown when the window displays a
volume. If this button is toggled on, only the underlay volume is
shown. This option has been added to assist in segmentation
volume voxel editing where the Main Window contains an anatomical
volume overlayed with the segmentation volume.
- (15 Nov 2006) Had some problems with exceptions messages (such as
an error reading a file) displaying incorrectly. Replacing
C-character strings with QStrings seems to have fixed the problem.
- (15 Nov 2006) Fixed some paint file reading error messages.
- (14 Nov 2006) Fixed reading of NIFTI volume file when the
orientation is not X={L,R}, Y={P, A}, Z={I, S}, such as AIL, so that
the voxel sizes and spacing are correctly set.
- (14 Nov 2006) When creating an MPEG1 or MPEG2 movie, check to see
if the movie file name is writable. If not, pop up an error
message. Unfortunately on MS Windows, if the file is writable but
the directory is not writable, QT still reports the file as
writable. The MPEG encoder will then crash Caret when it tries to
open the movie file.
- (13 Nov 2006) Looked into a problem with the colors being
incorrect in the temporary images used to create a movie file with the
program mpeg_create on MS Windows. The problem is that the bytes
are being written in the wrong endian when writing the temporary PPM
image file. However, the program mpeg_create expects them to be
in this incorrect order, so, fixing the writing of the PPM images
cannot be done as mpeg_create would no longer work correctly.
- (10 Nov 2006) When saving a foci file, allow the user to choose
saving of the original stereotaxic coordinates or the coordinates of
the foci projected to left and/or right surfaces.
- (10 Nov 2006) When a node is identified on a surface in a window,
also show the coordinates of that node for surfaces displayed in other
windows.
- (09 Nov 2006) Fix error message for PALS foci projection when the
foci's coordinate is invalid. Remove debug print message when
saving a foci file.
- (07 Nov 2006) Change version to
5.502.
- (07 Nov 2006) Made a changes to Flatten Full Hemisphere so that
there are not two compressed medial wall surfaces at the step in which
the medial wall and cuts are edited.
- (07 Nov 2006) When saving a topology file, default the topology
file selected in the Save Data File Dialog to the topology file used by
the main window surface.
- (06 Nov 2006) When reconstructing contours into a surface, create
a section file containing the sections corresponding to the nodes.
- (06 Nov 2006) Popup a message when cleanup contours is run.
- (06 Nov 2006) Fix View Current Files dialog so that border files
are not always listed, even when no borders are loaded.
- (06 Nov 2006) When a node was identified Caret was not updating
the toolbar in windows viewing volumes.
- (06 Nov 2006) When saving a foci file, allow the user to choose
both left and right surfaces for the unprojection of foci projections
into a foci file. Also, Caret was erroneously setting the file
modification status of the foci projection file when saving a foci file.
- (02 Nov 2006) When translating a surface using one of the Surface
Menu->Transform menu items, do not transform cells or foci since
they should be loaded as projection files.
- (02 Nov 2006) Fix setting of contour Z-coordinate when drawing
and reading contours.
- (02 Nov 2006) Add identification symbols to contours. If a
contour point highlighted and a surface is loaded, hightlight the
corresponding node in the surface. If a node in the surface is
identified, hightlight the corresponding contour point.
- (02 Nov 2006) Replace left/right hemisphere checkboxes with a
structure selection control on contour reconstruction dialog.
- (02 Nov 2006) Change colors of contours to a darker green.
- (01 Nov 2006) Add a cross at the origin of contour drawing.
- (01 Nov 2006) Inhibit the drawing of cells in their original
color and position when being aligned.
- (01 Nov 2006) Slow mouse speed used during contour alignment.
- (01 Nov 2006) Using a depth test for image drawing messed up
surface rendering (See 31 Oct 2006). Instead, set the Z-value for
the image near the far clipping plane.
- (31 Oct 2006) Fixed bug that caused contours to disappear that
were in the same section as that of a new contour being drawn while the
new contour was being drawn.
- (31 Oct 2006) Fixed bug that caused some contour cells to
disappear when new contours in a different section were being drawn.
- (31 Oct 2006) When drawing contours and only single section is
being displayed, set the selected to the section of the new contour
when drawing of the new contour is completed.
- (31 Oct 2006) If the contour number in the draw contour dialog is
changed, set the mouse mode to contour drawing.
- (31 Oct 2006) Add legends describing necessary mouse clicks to
Contour Set Scale Dialog. Fix setting of contour scaling.
- (31 Oct 2006) Add Hide All Contours to Contour Selection Dialog.
- (31 Oct 2006) Change image Z-value so that contours with negative
Z-values show up in front of the image.
- (30 Oct 2006) If mapping a NIFTI functional volume, add the
intention and TR to the metric column comment.
- (30 Oct 2006) Fix bug that caused Caret to crash if there were
contours loaded and an MDPlot file was imported without appending
selected.
- (27 Oct 2006) Add a Help button to the Display Control Dialog
that shows the dialog's help page.
- (27 Oct 2006) Add the title of the Main Window's current spec
file to the title of the Display Control Dialog.
- (27 Oct 2006) Fix determination of caret installation directory
for command line programs on Mac OSX.
- (26 Oct 2006) Fixed reading of CSV foci file Study Info Comments.
- (24 Oct 2006) Decrease the minimum scaling for contours so that
the user may zoom out further.
- (24 Oct 2006) Made fixes for reading MDPlot contour files.
- (24 Oct 2006) Rewrote and moved identification code into
BrainModelIdentification which is located in the BrainSet. This
eliminates code duplicated in WebCaret and results in WebCaret showing
the exact same text as Caret when an item is identified.
- (20 Oct 2006) Add image comparison (-image-compare) to
caret_command.
- (19 Oct 2006) Add a flag to the BrainSet that is only set by
WebCaret. If set and a scene file is read, paths associated with
any file listed in the scene file will be removed. This is
because SuMS stores all files associated with a spec file in a single
directory.
- (19 Oct 2006) Modifiy
caret_command so that if it is run with
"-help", a list of all of the commands is displayed. Running
caret_command with "-help-full" will show full information on each
command.
- (19 Oct 2006) Modify caret_command's "-show-scene",
"-show-surface", and "-show-volume" so that the volume file is
optional, and, if not specified, the image of the scene/surface/volume
is not saved in a file but is displayed in a window on the user's
display.
- (19 Oct 2006) Add "-image-view" to caret_command which displays
an image file in a window on the user's display. Due to a
limitation on Macs (the program is built as a simple executable and not
a Mac Application), scrollbars are available only on Linux and Windows.
- (19 Oct 2006) Add "-show-volume"
to caret_command which generates
an image of a volume.
- (18 Oct 2006) When saving a scene, save the width and height of
the OpenGL widget so that it may be used later when caret_command
cxommands a scene for diplay. This ensures that the window size
exactly matches the width and height of the saved window.
- (13 Oct 2006) Add "-show-scene"
to caret_command with
renders the main window image of a scene to an image file.
- (13 Oct 2006) When constructing a BrainSet from a topo/coord file
pair, set the BrainSet's structure to that of the coord file.
- (13 Oct 2006) Fix Spec File's remove paths from filenames.
- (13 Oct 2006) Add
"-show-surface" to caret_command which
generates an image of surface in one or all of the standard views.
- (12 Oct 2006) Make color names in the color key dialog appear as
hyperlinks if vocabulary information is available.
- (11 Oct 2006) Simplify cropping on the image editor window.
- (11 Oct 2006) Fix default file naming for border and border
projection files.
- (11 Oct 2006) Use QT's QFile::errorString() when Caret is unable
to read or write a file.
- (04 Oct 2006) Fix removal of watch cursor when loading a border
file through the open data file dialog.
- (03 Oct 2006) Add an optional "point radius" to border and border
projection links that will be used, in some cases, a variability
measurement. Add two new Border Drawing modes that show the
border link variability with or without connected line segments.
- (03 Oct 2006) When generating average borders, also add a
variability measurement to the links of the average border.
- (03 Oct 2006) Add -surface-border-variability to caret_command
that resamples a border file so that the borders have the same number
of links as borders with corresponding names in another border file and
set the variability.
- (03 Oct 2006) Add -surface-border-nibbler to caret_command that
remove links from a named border in a border file. The user may
use a surface node or extrema to set a plane used for removing links.
- (03 Oct 2006) Add -surface-border-extrema that lists the extrema
(bounds) for a surface and a border in a border file and also shows the
difference.
- (27 Sep 2006) Fixed a bug with editing the comment in a
multi-brick volume file on disk using the data file comment editor from
the Open Data File Dialog. The bug resulted in the volume
containing only one brick instead of all of the bricks in a multi-brick
volume file. Now, none of the bricks are lost.
- (27 Sep 2006) Fixed a bug that caused Caret to crash if a
probabilistic atlas volume with only one channel was loaded.
- (26 Sep 2006) Modify the node attribute selection combo box to
prevent problems with it if there is more than one spec file loaded.
- (25 Sep 2006) Add a new toggle
button, labeled "S", to the toolbar that is displayed when viewing a
volume. When the button is toggled on and the volume is being
viewed in an orthogonal axis, the slice numeric controls instead show
stereotaxic coordinates.
- (25 Sep 2006) Use common widget for entering and editing studies
for foci and vocabulary.
- (25 Sep 2006) When loading a file via the Toolbar's "Spec"
button, only ask Append/Replace if there is data of the corresponding
type loaded.
- (25 Sep 2006) Change Caret version to 5.501.
Release Caret 5.5 (22 September 2006)
- (22 Sep 2006) Add Layers->Borders->Create Borders From
Paint Regions which creates borders around all paint regions in a
selected column. It will probably work best on a surface with a
closed topology.
- (20 Sep 2006) Fix setting of column names for old, old, version 0
paint files.
- (20 Sep 2006) Change Layers->Foci->Delete Non-Displayed
Foci to "Delete Foci Not Displayed on Main Window Surface". When
choosing foci for deletion, also use status of show foci on correct
hemisphere only option.
- (20 Sep 2006) Fix problem with reading files containing long
lines. This problem was traced to a bug in Trolltech's QT
Software (http://www.trolltech.com/developer/task-tracker/index_html?method=entry&id=104776)
which would only read the first 4095 characters in a line. So,
any files with lines longer than 4095 were not read correctly.
- (19 Sep 2006) When creating a new spec file on the spec file
dialog, close current spec file and reopen the new spec file into a new
spec file dialog.
- (19 Sep 2006) Require a volume's existing voxel sizes to be
positive and the resampling voxel sizes to be positive.
- (19 Sep 2006) When saving a volume file using the Save Data File
Dialog, default the volume to the volume of the selected type that is
selected on the Display Control Dialog's Volume - Overlay/Underlay page.
- (19 Sep 2006) Enable double-clicking of a cell in the file
viewing table for editing the cell's contents in a text editor.
- (19 Sep 2006) Multi-Fiducial Metric Mapping changes: (1) Default
column names are now AFM for average fiducial mapping and MFM for
multi-fiducial mapping. When available, include hemisphere in
column name. (2) Default comments are now "Average Fiducial
Mapping (AFM)" and "Multi-Fiducial Mapping (MFM)". (3) The cells
in the metric naming table may be double-clicked to display and more
easily edit the cell's text.
- (15 Sep 2006) Fixed writing of cell/foci files in Comma Separated
Value (CSV) file format.
- (15 Sep 2006) Fixed bug that produced some print statements when
saving a border file.
- (14 Sep 2006) Change key command used to capture an image of
caret dialogs to CTRL + SHIFT + F1.
- (14 Sep 2006) Fixed crash that occurred if capturing an image of
part of the main window but without any of the main window selected.
- (12 Sep 2006) Improve text editor with better search
options. Pressing the Find toolbar button brings up a dialog for
searching and replacing include case sensitive and backwards searches.
- (12 Sep 2006) Add generation of a border grid for analysis with a
third party program.
- (12 Sep 2006) Add foci highlighting. A focus is highlighted
by clicking on the foci's color in the Foci Color Key Dialog.
- (12 Sep 2006) Add vocabulary abbreviations to name selection
dialog.
- (12 Sep 2006) Fix Surface->Transform->Apply Current View
when both translation and rotation were applied.
- (12 Sep 2006) Got shell command window to work on Windows.
- (11 Sep 2006) Modify Interpolate Surfaces so that it applies the
current view to the surfaces used for interpolation.
- (11 Sep 2006) Fix Edit Paint Names Dialog.
- (11 Sep 2006) Fix deletion of probabilistic atlas file on view
current files dialog.
- (11 Sep 2006) Save override border colors with area colors to
scene.
- (11 Sep 2006) Correct Metric/Shape statistics dialogs that
mistakenly read "Type II Error" but should have been "Type I Error".
- (08 Sep 2006) Change version to
5.5.
- (08 Sep 2006) Add Vocabulary Editor to Attributes Menu. If
the user clicks on a name in a color key and there is a corresponding
entry in the vocabulary file, information from the vocabulary file will
be displayed in the Identify Window.
- (07 Sep 2006) Made some changes to reading of cells/cell
projections from comma separated value files.
- (06 Sep 2006) Have Identify Window's CID button clear both border
highlighting in addition to node highlighting.
- (05 Sep 2006) Change border and paint color keys so that if the
user clicks on the color swatch, the nodes are highlighted or the
border point/line size is doubled. Clicking on the color swatch
of a highlighted item turns of highlighting. Add item to
Layers->Borders menu and popup menu to clear border highlighting.
- (05 Sep 2006) Add menu item to Attributes->Vectors Menu that
copies the main window surface's normal vectors to the surface vector
file.
- (01 Sep 2006) Fixed scene problem with node attribute files
(metric, paint, etc.) when the number of surfaces loaded exceeded the
number of columns in the node attribute file.
- (01 Sep 2006) When generating an areal estimation file, add the
border file and uncertainty value to the comment.
- (01 Sep 2006) Increase far and near values for orthographic
projection so that the surface does not get clipped as quickly and user
can zoom in further.
- (01 Sep 2006) Add coordinate files for PALS SPM95 and SPM96 to
mapping files for use by PALS foci projection.
- (01 Sep 2006) Add SPM96 and MACAQUE_F6 to stereotaxic spaces.
- (31 Aug 2006) Add color key displays to the popup menu.
- (31 Aug 2006) Add color key windows to scenes.
- (31 Aug 2006) Add an areal estimation page to the Display Control
Dialog so that column names may be changed.
- (31 Aug 2006) Add Color Keys for Areal Estimation, Probabilistic
Atlas, Volume Paint, and Volume Probabilistic Atlas.
- (30 Aug 2006) Add option to Display Control Dialog's Border Page,
that overrides border colors with area colors.
- (30 Aug 2006) Upgrade QT on Mac to 4.1.4.
- (30 Aug 2006) Add some additional file filters to the text
editor's open/save dialogs.
- (29 Aug 2006) Fixed file filters so that existing files are
displayed on Capture Image of Main Window Dialog's file selection
dialog.
- (29 Aug 2006) Increase width of scene selection box on Display
Control Dialog.
- (29 Aug 2006) Move "CID" button (clears ID symbols from surface)
to the left side of the Identify Window so that is easier to access.
- (29 Aug 2006) Modify interpolate surfaces dialog so that the
number of surface selections is equal to the number of surfaces that
are loaded.
- (29 Aug 2006) Fix problem with the surface radically changing
size at the end of the interpolate surfaces action.
- (29 Aug 2006) Add color key
dialog for borders, cells, foci, and paint. The color key dialog
shows the names of all displayed items and a swatch of the assigned
color.
- (28 Aug 2006) Add a new metric selection option on the
Display Control Dialog. If the "L-to-L, R-to-R Matching..."
checkbox is selected and the user selects a metric column, look
in the selected column's name for "left" (or "right") and and apply it
to all left (or right surfaces). Then, find the corresponding
column for the other hemisphere and apply it to the remaining surfaces.
- (28 Aug 2006) Fixed saving of Paint Medial Wall Override to a
scene.
- (11 Aug 2006) Add spherical deformation to the caret_command
command line program.
- (11 Aug 2006) Add optional surface shape file that will contain
uncertainty to caret_command -surface-average.
- (11 Aug 2006) Add item to Layers->Foci menu that deletes all
colors that do not match the start of any foci name.
- (10 Aug 2006) Add a Surface Distance metric/shape test to the
Metric/Shape Statistical operations menu.
- (09 Aug 2006) Add surface smoothing to caret_command.
- (09 Aug 2006) Add item to Layers->Foci menu that deletes all
non-displayed foci.
- (07 Aug 2006) In metric/shape statistical operations, use the
topology file specified by the user. Note: some coordinate files
contain the name of a topology file in the header that is automatically
loaded and assigned to the coordinate file when the coordinate file is
loaded.
- (04 Aug 2006) Add button on Display Control's Scene Page "Create
Spec From Selected Scenes" which prompts the user for a scene file name
and a spec file name. This creates a new scene file containing
only the selected scenes and a spec file containing the files from the
selected scenes.
- (04 Aug 2006) Change Check All Scenes so that it unloads all file
prior to estabilishing a scene.
- (04 Aug 2006) Fix ID window text problem that resulted in new
text being blue and underlined if a hyperlink had been clicked.
- (03 Aug 2006) Add a new surface shape selection option on the
Display Control Dialog. If the "L-to-L, R-to-R Matching..."
checkbox is selected and the user selects a surface shape column, look
in the selected column's name for "left" (or "right") and and apply it
to all left (or right surfaces). Then, find the corresponding
column for the other hemisphere and apply it to the remaining surfaces.
- (03 Aug 2006) Change message on Display Control's Scene page when
unloading all files but spec and scene.
- (03 Aug 2006) When a focus is identified, display its position on
all fiducial surfaces with valid stereotaxic spaces.
- (03 Aug 2006) Fix crash if trying to access a color but no colors
are loaded during probabilistic atlas coloring.
- (03 Aug 2006) Fix normal/threshold probabilistic atlas selection
on Display Control.
- (03 Aug 2006) Remove min/max section numbers from Main Window
Status Bar.
- (03 Aug 2006) Change cell and foci left/right display to a single
check box Show Cells/Foci on Correct Surface only.
- (01 Aug 2006) Add section control to scenes.
- (01 Aug 2006) Do not require a class when entering foci on the
map stereotaxic foci dialog.
- (01 Aug 2006) Transformation Matrix Dialog, attempt to get new
matrices created with oblique volume views to work.
- (01 Aug 2006) When a voxel is identified in volume montage
display, center the selected volume slice in the montage.
- (31 July 2006) Fix voxel identification for volume montage
viewing mode.
- (31 July 2006) Change volume montage slice orders to that the
slices increase going right to left and then down to the next row of
slices.
- (31 July 2006) Allow main window transformation axes to be turned
on/off by clicking on the axes in any of the viewing windows.
- (31 July 2006) Make volume crosshairs consistent so X is red, Y
is green, and Z is blue.
- (28 July 2006) Add projection
of Foci to PALS atlas. Foci
are mapped to the surface that is in the same stereotaxic space as the
focus.
- (27 July 2006) Fix shortcut keys for Identify and Transformation
Matrix Editor menu items on Windows menu.
- (27 July 2006) On transformation matrix editor and applying a
transform, have cancel button cease the process.
- (24 July 2006) Add Levene's Test for Equality of Variance to
Metric/Shape Statistical processing.
- (24 July 2006) Use Dcdflib for statistical P-Value computations (http://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware.aspx?Software_Id=21).
- (21 July 2006) Reorganize/rewrite statistical functions and
place them in their own library.
- (18 July 2006) Make text boxes for scene names wider on Display
Control Dialog.
- (18 July 2006) Add item to
Caret Help Menu to search the Caret website.
- (18 July 2006) Fix default directory selection on Copy Spec File
Dialog and add a previous directory selection.
- (18 July 2006) Add comment button to Spec File Dialog.
- (18 July 2006) Upgraded the
Linux version of QT to 4.1.4. This appears to correct a bug that
caused Caret to crash on startup when the style being used was
Plastique. Only some Linux systems default to the Plastique style
and I do not know how this is chosen.
- (18 July 2006) Added preliminary support for storing cells and
foci as comma separated value (CSV) files.
- (14 July 2006) Fixed computation of P-Values when the T-Value is
less than zero.
- (13 July 2006) When using the CTRL-Escape Key (Apple-Escape Key
on Macs) which captures an image of any caret dialog or window, allow
the user to choose to copy the image to the clipboard, print the image,
or save the image to a file.
- (13 July 2006) Add one more bucket to histogram so that all
values are shown (largest value was at left side of last bucket).
- (13 July 2006) Make range of X-min/max unlimited on graph dialog.
- (13 July 2006) Add False Discovery Rate to T-Map generation
dialog (this may get changed soon).
- (12 July 2006) Fix crash when displaying Volume Region of
Interest Dialog.
- (12 July 2006) Fix surface shape clustering and smoothing.
- (11 July 2006) Add help buttons to metric/shape statistics
dialogs that link to appropriate help page.
- (10 July 2006) Change style of Caret data file XML headers to
remove limitations on header tag name characters.
- (10 July 2006) Add some additional stereotaxic spaces: T88, SPM,
SPM95, SPM5.
- (07 July 2006) Add comment section to Create Spec File Dialog and
SureFit Segmentation Dialog. Add View/Edit comment to Open Spec
File Dialog.
- (07 July 2006) Add ticks in second plane for surfaces axes and
add an offset for the surface axes controlled through the Display
Control's Surface Miscellaneous page.
- (07 July 2006) Mac OSX Only - Modify QT source for Q3FileDialog
to set the style of the Filter Combo Box to Plastique since Mac style
is way to long and stretches off the screen.
- (07 July 2006) Fix error that made histogram dialogs modal.
- (07 July 2006) Allow Set Topology Dialog to remain displayed at
all times instead of closing upon topology selection.
- (05 July 2006) Change the decimation algorithm from
vtkDecimateCaret to vtkDecimatePro. vtkDecimate was dropped from
VTK version 5 so I converted it to work with VTK5 but it was difficult
to control the polygon count and it is a patented algorithm.
vtkDecimatePro produces very similar surfaces with a slightly smaller
polygon count the VTK4's vtkDecimate. vtkDecimatePro is easier to
use with non-human surfaces and there are no patent issues with
vtkDecimatePro.
- (05 July 2006) Fixed bug in the math utilities function
signedDistanceToPlane when converting floats to doubles in order to
call a VTK math function. This bug caused a problem with sulcal
depth generation.
- (05 July 2006) Add option (defaulted on) to the Spherical
Deformation Dialog to enable one iteration of smoothing of deformed
coordinate files (except flat coordinate files). Previously, one
iteration of smoothing was always performed. Option also added to
Apply Deformation Map Dialog.
- (03 July 2006) Surface
Registration Fixes: First, when creating the deformation map file,
indicate the type of surface (flat or spherical) to
BrainModelSurfacePointProjector so that it can properly projection
target nodes onto the deformed source surface. Second, the
deformation map file always has the closest of the three source nodes
listed first. When the first node was not the closest, the nodes
and barycentric areas were being swapped but the barycentric areas were
not properly swapped. These problems were first noticed when the source
surface had far fewer nodes than the target surface.
- (30 June 2006) Add Caret Tips Window which is selectable from the
Help Menu and is automatically displayed (but can be disabled) after
loading the first spec file in a caret session.
- (30 June 2006) Update graphics window's popup menu.
- (29 June 2006) Update the Mac Application for File Open Event.
Release Caret 5.402 Update (29
June 2006)
- (29 June 2006) Fix Display Control's Surface Shape Min/Max
mapping spin boxes so that they allow negative values
- (28 June 2006) Now version
5.402.
- (28 June 2006) Fixed bug that
caused the current directory to be set to the caret installation
directory during SureFit Segmentation. This typically occurred if
caret was started in a directory other than the directory containing
the volume for segmentation such as on Window when double-clicking a
shortcut to Caret on the Desktop.
- (28 June 2006) Allow several surfaces, in addition to the average
fiducial, to be shown over the volume slices.
- (27 June 2006) Add variance smoothing to metric and shape file
statistical operations.
- (27 June 2006) Copied and
modified VTK's vtkMPEG2Writer class so that it writes MPEG1 video
files. This allows Mac users to create MPEG movies that are
playable by the standard version of QuickTime media player. It
also eliminates the need to use the command line program mpeg_create to
create movies although it is still supported. This will also help
windows users since mpeg_create often crashed or hung when creating
movies.
- (26 June 2006) Added an active hull surface that may be displayed
over volume slices.
- (26 June 2006) Updated caret_command to combine surface shape
files.
- (26 June 2006) Added Surface->Measurements->Generate
Distance: Surface A to Surface B which creates a surface shape column
that contains the three-dimensional distances between two surface's
coordinates.
- (23 June 2006) Added MPEG2 movie writing using a VTK class.
At this time, only the latest Windows Media Player run on MS Windows
and mpeg2play on Linux can play MPEG2. According to Apple, an
upgrade to Quicktime (that cost $) will allow Quicktime to play MPEG2
movies.
- (22 June 2006) Change File Menu's "Record as MPEG" to "Record
Main Window Images as Movie".
- (22 June 2006) If the user attempts to map an ".hdr" volume to a
surface, warn the user that the volume must contain an SPM originator
to be mapped correctly.
- (22 June 2006) Enable/Disable menu items using QT4.
- (22 June 2006) Replace
vtkDecimate with vtkDecimateCaret since
vtkDecimate was dropped from VTK5. There might be polygon
reduction issues with rodent brains. Upgrade to VTK5.
- (21 June 2006) Replace QtFloatSpinBox with QDoubleSpinBox.
- (21 June 2006) Compiled with QT3 support off to eliminate calls
to class methods that are not QT4 compatible. QT4 conversion will
be complete once additional widgets can be added to QFileDialog.
- (19 June 2006) When text added to Identify Dialog automatically
scroll to the bottom of the text.
- (19 June 2006) Fixed loss of cell class information when
projecting or unprojecting.
- (16 June 2006) Add capture of 6 standard view image to Capture
Image of Main Window Dialog.
- (16 June 2006) Upgraded Recording Dialog to QT4.
- (16 June 2006) Add a page to
the SureFit Segmentation Dialog that
shows the current directory and prevents the user from continuing if
the current directory is the caret installation directory. The
current directory may be the installation directory if Caret was
started by a shortcut on the Windows Desktop or from the Mac's Dock.
- (16 June 2006) Add a menu item for reverse the order of points in
a contour.
- (15 June 2006) Added drawing modes for contours so that contours
may be drawn as lines, points, or points and lines. If drawing
the first contour point in red, make the first contour point size
double that of the normal contour points.
- (15 June 2006) Fixed crash that occurred when adding a new color
using the Edit Colors dialog.
- (15 June 2006) Upgraded SuMS Database Dialog to QT4.
- (15 June 2006) On Surface to Volume Dialog, change "Thickness
Step" to "Intersection Step".
- (14 June 2006) Now version 5.401.
- (13 June 2006) Added identification of contours and contour cells
in view mode. Enhance legends for contour append mode.
- (13 June 2006) Upgraded code for Map Volumes To Surfaces to QT4.
- (12 June 2006) Upgrade to QT 4.1.3. This seems to have
corrected problems with windows popping up under the current window on
Macs and fixed directory selection problems when using Set Current
Directory from the File Menu.
- (09 June 2006) Fix problem with copy/zip spec file when the
volume consisted of a header file and a volume file and the volume was
in a different directory than the source spec file.
Release version 5.4 (09 June
2006)
- (09 June 2006) Destroy the SureFit Segmtation Dialog when it is
closed so that segmentation can be restarted without having to exit and
restart caret.
- (08 June 2006) Version 5.4
- (08 June 2006) Handle http URL's in Caret web help by displaying
the page in a web browser.
- (07 June 2006) Fixed writing of gzipped volume files on Windows
by updating the zlib library and using buffered writing instead of
unbuffered writing.
- (05 June 2006) On Volume Math Dialog, change "Volume C" to
"Volume Output".
- (05 June 2006) When loading a scene, do not load any scene file
from the spec file saved within the scene.
- (05 June 2006) Move shape file statistical processing from
Surface Shape Menu to new Metric and Shape Statistical Processing Menu.
- (05 June 2006) Save data file timeout from SuMS Dialog in the
preferences file.
- (05 June 2006) When adding a new color, place it in its name
sorted position.
- (02 June 2006) Correct problem with uploading volume data files
to SuMS.
- (02 June 2006) Add one-sample and two-sample T-Tests for Metric
and Surface Shape.
- (01 June 2006) Correct problems with interpolate surfaces not
updating the model in the main window.
- (31 May 2006) When displaying a scene, do not let viewing windows
to be shown off the screen.
- (30 May 2006) When mapping to the Average Fiducial Surface, set
the column threshold to the threshold entered for the respective
functional volume.
- (30 May 2006) Correct uploading of volume data files to SuMS.
- (25 May 2006) Add NIFTI gzipped file to volume files supported by
script builder.
- (25 May 2006) Disable image file save dialog if there are no
image files loaded.
- (23 May 2006) Fix writing of WU NIL volumes on little endian
architectures (Intel x86, typically windows and linux).
- (22 May 2006) Fixed problem with loading a Hull Coord File using
the Open Data File Dialog.
- (22 May 2006) Added scroll bars to Volume Math Dialog since
dialog was getting too tall.
- (18 May 2006) Added missing '*' to .ifh volume file filters.
- (18 May 2006) Add update deformation path, create spec file, and
add file to spec file to the script builder.
- (18 May 2006) Remove message about undo stack size printed when
editing segmentation voxels.
- (17 May 2006) Now version 5.332.
- (17 May 2006) Fix display of web page when a hyperlink is clicked
in the file comment editor (QT4 upgrade problem).
- (17 May 2006) Make sure a display list is valid prior to deleting
it.
- (17 May 2006) Remove multiple sets of scrollbars from Display
Control Dialog.
- (16 May 2006) Add Clean Up Contours to the Layers->Contours
menu. Clean Up Contours will remove consecutive, duplicate points
from contours and it will remove contours with less than 3
points. These types of contours cause problems during
reconstruction.
- (16 May 2006) Replace line edits with spin boxes on Surface to
Volume Dialog..
- (16 May 2006) Restore volume animation that was broken during
upgrade to QT4.
- (16 May 2006) When adding a volume file entry to a spec file,
only write the data file name if it is different than the header file
name (ie: NIFTI volume is stored within a single file).
- (16 May 2006) Scene modifications: track volume oblique slice
sampling size and the matrices associated with transformation data
files.
- (15 May 2006) NIFTI volume
reading and writing including zipped files, paint volumes, and support
for the AFNI extension.
- (12 May 2006) Add "plus_" and "minus_" to name in the paint
created by the Find Significant Clusters operation.
- (12 May 2006) Fixed bug that prevented mapping to average
fiducial surface using the map volume to surface dialog.
- (09 May 2006) Fix spec file update when the volume header file
name is the same but the data file name changes.
- (03 May 2006) When page selection changed on Display Control
Dialog, scroll the page to the left and top.
- (02 May 2006) Corrected problems with left hemisphere foci not
appearing.
- (27 April 2006) Improved support for reading and writing NIFTI
volume files.
- (21 April 2006) Eliminated all
QT 3 version support code from the Display Control Dialog. This
appears to have corrected two problems. The first correction
eliminates lots of little windows (border names, colors, foci, etc
checkboxes) from appearing prior to the Display Control Dialog.
The second correction appears to eliminate the very slow time (minutes)
that elapsed while displaying the dialog on computers with limited
amounts of memory.
- (17 April 2006) Add option to caret_command that sets the source
and target paths.
- (13 April 2006) Now version
5.331.
- (12 April 2006) Fixed bug found in shape file T-Map calculation
that occurred if the first shape file had fewer columns that the second
shape file.
- (04 April 2006) Replace Volume Animate start/resume/pause/stop
with a single Animate button that goes through all slices. This
change has been made because the volume animate thread does not
work in QT4.
- (03 April 2006) Fix triangle area calculation that was replaced
vtk's triangle area a few days ago.
- (03 April 2006) Fixed problem with bizarre characters in surface
region of interest report.
- (31 March 2006) Fix editing of file column comments.
- (31 March 2006) Move Image Editor and Text File Editor menu items
from the File Menu to the Window Menu.
- (31 March 2006) Fix initial directory on Zip Spec File dialog's
choose zip file button.
- (31 March 2006) Replace use of function tmpnam() and replace with
QDir::tempPath(). tmpname() is a possible security hole.
- (31 March 2006) Add printing, font selection, and search/replace
to text editor.
- (31 March 2006) Fix creation of wrong column on metric/shape
inclusive range operations.
- (29 March 2006) When merging contours, beep if a contour is not
selected with a mouse click. In addition, when two
contours are merged, resample the new contour so that the region
between the contours will contain points.
- (29 March 2006) Started adding an "index tree" to the help window.
- (27 March 2006) Fixed problems with absolute paths that should
not have been on files added to the spec file in the windows version of
caret.
- (27 March 2006) For file open/save/import/export dialogs, set the
directory to the current directory.
- (27 March 2006) Add application of a deformation map to a data
file to caret_command.
- (24 March 2006) Fix selection of contour cells when aligning a
region of a contour.
- (24 March 2006) Change contour region box from solid to outline
so that contours/cells are visible.
- (24 March 2006) Warn that contour region alignment will not
function if contours are rotated.
- (24 March 2006) Fix writing of WU ".ifh" header files.
- (17 March 2006) Fix reading of version 1 cell projection files.
- (17 March 2006) Fix bug that failed to create new metric/shape
column in mathematical operations.
- (17 March 2006) Work around QT4 bug that prevented reading of
version 0 cell files.
- (17 March 2006) Fix bug with missing items on image editor resize
dialog.
- (16 March 2006) Force all volumes written by surefit segmentation
process to be written as floats.
- (16 March 2006) Fixed Display Control images selection page on
windows.
- (16 March 2006) Work around QT4 bugs for SuMS file transfers.
- (13 March 2006) Fixed bug that prevented writing a file when the
all files preferred write type and the files read type were the same
but not acceptable for an output format.
- (13 March 2006) Fixed crash when combine paint volumes was
selected on Volume Mathematical Operations Dialog.
- (13 March 2006) Third volume optional on volume math with script
builder.
- (13 March 2006) Shrank font for node number on ID dialog.
- (13 March 2006) Fixed bug on script builder that prevented
creating the script without executing the command.
- (13 March 2006) Fixed crash that caused Caret to crash when
saving a coordinate file.
- (10 March 2006) Fix bug that listed an invalid cerebral hull
volume as a segmentation volume.
- (10 March 2006) Fixed script builder.
- (10 March 2006) Put updated mingwm10.dll in windows distribution.
- (09 March 2006) Since caret cannot handle scenes with more than
one spec file, do not allow a scene to be created if there is more than
one spec file loaded.
- (09 March 2006) Add checks for invalid surface type or topology
type when importing a surface file.
- (09 March 2006) Add generation of sulcal depth to caret_command.
- (07 March 2006) Fix crash when loading a paint file for a
scene. This is a QT4 bug.
- (07 March 2006) Fix missing Metric Mathematical Operations.
Release Version 5.33 03 March 2006
- (03 March 2006) Fixed display of caret help on Windows.
- (03 March 2006) Changes to set directory dialog.
- (03 March 2006) Fix crash when space button pressed on Create
Spec File Dialog.
- (02 March 2006) Move caret_morph command line program operations
in caret_command.
- (01 March 2006) Add projection and unprojection of cell and foci
data.
- (01 March 2006) Add projection and unprojection of borders to
caret_command program.
- (01 March 2006) Add new dialog for
capturing an image of the main window to the file menu. The menu
item is named Capture Image of Main Window. The dialog allows the
user to capture an image of the entire main
window or a region selected with the mouse. The captured image
may be
copied to caret's loaded images, copied to the clipboard so that it can
be pasted into other programs, printed, and/or saved to a file.
- (27 Feb 2006) Update Linux compiler to GCC 4.0.2 with static
libraries to fix crash on some Linux systems with shared object
libraries different that out build system. This fixes the failure
to catch exceptions that were thrown.
- (24 Feb 2006) Fix crash in spherical deformation if the original
coordinate file contained a full path in its name.
- (24 Feb 2006) Default align sphere checkbox checked on align
surfaces dialog.
- (22 Feb 2006) Add conversion between caret paint file and free
surfer label files to caret_file_convert.
- (21 Feb 2006) Add ability to generate inflated, ellipsoid, et al
using caret_command.
- (21 Feb 2006) Add generation of hull surface when determining
sulcal depth.
- (21 Feb 2006) Added some kludges to get around bugs in QT4.1 that
prevented writing caret files in binary format. All file writing
preference to be set to binary.
- (20 Feb 2006) Figured out how to create simple executables for
command line programs on Mac OSX instead of app bundles.
- (14 Feb 2006) Replace "QtPlot" graphs with Qwt graphs.
- (13 Feb 2006) The QT4.1 bugs
appear to also cause problems with writing files in binary
format. So, for now, the preferences always report that the user
wants to write ASCII format files.
- (13 Feb 2006) There are bugs in the QT4.1 software that cause it
to report invalid file read position and end of file status. Code
has been added to Caret5 to get around this bug until Trolltech (the
writer of the QT software) corrects the problem. All of the added
code is within "#define QT4_FILE_POS_BUG".
- (13 Feb 2006) For all color files, add the color for "???", the
unknown color, when the first color is added to the color file.
- (10 Feb 2006) Modify caret_command so that it can add files to a
spec file.
- (09 Feb 2006) List the name of the spec file on the File Menu's
Close Spec File menu item.
- (07 Feb 2006) Convert SpecFile dialog and other dialogs to QT4 to
fix problems on Windows.
- (06 Feb 2006) Fixed problem with JPEG and QT 4.
- (06 Feb 2006) Added a FreeBSD version of Caret5 to the download
page. This version was built by Jason at MCW.
- (06 Feb 2006) Limit sizes of dialog windows to less than the
height of the desktop.
- (06 Feb 2006) When a scene is selected, do not alter the main
window and position other windows relative to the main window.
- (06 Feb 2006) Add selection for surface and topology types on
Import Data File dialog.
- (01 Feb 2006) Add importing of Free Surfer binary format "curv"
files.
- (01 Feb 2006) Add importing of Free Surfer binary format "w"
(weight, functional) files.
- (01 Feb 2006) Add importing of Free Surfer binary format surface
and surface patch files.
- (31 Jan 2006) Replace FileOperationException and FileIOException
with FileException.
- (31 Jan 2006) Make some qmake .pro fixes for the elimination of
Borland C++.
- (30 Jan 2006) Split toolbar into two rows with model selection
control in the bottom row.
- (30 Jan 2006) Modify file reading to throw exception if reading a
binary format Caret file due to a bug in QT4. Similar problem
with version 0 topology file.
- (30 Jan 2006) Modify the multi threaded algorithm class to avoid
unlocking mutexes due to a bug in the QT4 windows software.
- (27 Jan 2006) Change Identify Sulci process in SureFit
Segmentation. When determing the sulci for paint geography, use
the CerebralHull.erode.3 volume (the cerebral hull eroded three times)
instead of Sulci.3.dilate.
- (26 Jan 2006) In Segmentation voxel editor, the size of "undo's"
was unlimited. Now, the total "undo" size is limited to 10 Meg
with a minimum of one item. This will hopefully fix some crashes
that have occurred during voxel editing.
- (26 Jan 2006) Correct problem in error measurements at beginning
of automatic error correction noticed on Windows.
- (24 Jan 2006) Add item to surface menu that creates a
segmentation volume from a surface.
- (24 Jan 2006) Move script builder from Volume Menu to
Window Menu. Command line program caret_volume has been renamed
to caret_command since it now performs non-volume operations.
- (23 Jan 2006) Prevent possible crash in TopologyHelper with a
nodes that has zero neighbors. Crash is noticed on Windows Caret
while creating inflated surfaces.
- (13 Jan 2006) Add support for universal binaries (power pc and
intel architectures) for Mac OSX.
- (12 Jan 2006) Upgrade Caret5 to
use user interface software QT
4.1 (www.trolltech.com). Caret5 runs but a QT bug prevents proper
file reading.
- (11 Jan 2006) Replace all uses of std::string with QString.
- (06 Jan 2006) Add ability to
load multiple spec files into Caret. All brain models are
available for display. In addition, if multiple spec files have
been loaded and there are at least two active fiducial surfaces, add a
selection to show all fiducial surfaces simultaneously.
- (04 Jan 2006) Correct 3D border drawing when metric and/or shape
color palette bars are displayed.
- (01 Jan 2006) Happy New Year !!!
- (30 Dec 2005) Remove widget names from QT constructors in
preparation for conversion to QT4.
- (29 Dec 2005) Fixed bug in caret_volume and Caret's Volume
Mathematical Operations that always caused a non-matching dimensions
error.
- (29 Dec 2005) Remove OSX_COMPILER_BUG stuff since compiler on Mac
was fixed long ago to properly initialize std::string that are a static
member of a class.
- (29 Dec 2005) Consolidate stereotaxic space, species, category,
and structure code.
- (28 Dec 2005) Changes made to SpecFile code internals to support
multiple structures.
- (23 Dec 2005) Add optional distortion correction via a metric
column for surface region of interest statistical report.
- (20 Dec 2005) Fixed bug that caused a data file to be reported
modified when it had not been modified but just copied.
- (20 Dec 2005) For scenes, default window placement to leave main
window at its location but place all other windows relative to the main
window.
- (19 Dec 2005) Modified Interpolate Surfaces so that surface
scaling is interpolated. Previously, the scaling of the first
surface in the sequence was used for all surfaces in the sequence.
- (19 Dec 2005) Correct bug on Windows that caused problem with
Automatic Rotation Dialogs fixed rotation spin box.
- (19 Dec 2005) On Volume Attributes Dialog and Surface to Volume
Dialog there is an option to get paramters from a volume file.
This option now converts the parameters read from the volume file to an
LPI orientation.
- (15 Dec 2005) Fixed some problems that were found with NIFTI file
format during various Caret operations.
- (15 Dec 2005) When reading a VolumeFile and determining its file
type by using the file's extension, convert the extension to lowercase
since MS Windows or the SFTP client we use seems to sometimes make
".HEAD" files into ".head" files.
- (13 Dec 2005) Implement preliminary NIFTI Data File format for
Coordinates, Topology, Metric, Shape, Paint, and Probabilistic
Atlas. For Node Data files, each column is stored in a separate
piece of memory rather than one huge contiguous piece. The
NIFTI files may also be read and written in XML format.
- (2 Dec 2005) Install kludge to get around strange problem on
windows. Creating movies of a flat surface resulted in smeared
images. The problem was narrowed to the fact that lighting was
off. So, when capturing movies on windows of a flat surface, turn
lighing on prior to capturing an image of the flat surface and turn
lighting off after capturing an image of the flat surface.
- (1 Dec 2005) Add Find Interhemispheric Clusters to
Attributes:Surface Shape menu.
- (1 Dec 2005) Surface Shape Find Significant Clusters: allow
metric or shape file for distortion correction file.
- (1 Dec 2005) Fix install script on Mac OSX so that it does not
try to set permissions on the no longer existing "luts" directory.
- (30 Nov 2005) Show thresholds on Surface Shape Significant
Cluster report.
- (22 Nov 2005) Fixed problem with reconstruction of primate brains
from volumes with unusual voxel sizes on Windows. Solution was a
new version of VTK (see 17 Nov 2005).
- (22 Nov 2005) Add a new Palette, "PSYCH-NO-NONE", that is similar
to the PSYCH palette but does not have the NONE color.
- (22 Nov 2005) Fix metric coloring so that nodes that are between
pos-min and neg-min are not colored. Update labels on Display
Control to add ">" to pos-min and "<=" to neg-min.
- (22 Nov 2005) Surface Region of Interest Dialog: Add "And Not"
selection which selects nodes that are currently selected but NOT
selected in the new selection. Allow creation of new metric and
surface shape column when assigning the respective values.
- (22 Nov 2005) Surface Shape Find Significant Clusters: compute
degrees of freedom and p-value for t-map and only use the biggest
cluster from each of the shuffled t-maps.
- (18 Nov 2005) Add
non-uniformity correction to Edit Volume Attributes: Data page.
- (18 Nov 2005) Add surface offset to volume script builder's
Intersect Volume With Surface.
- (17 Nov 2005) Surface reconstruction from volume polygon
decimation is now optional but decimation is defaulted on. The
decimation algorithm is failing to work properly on one PC with several
primate species.
- (14 Nov 2005) Fix palette color bar for functional volume viewing.
- (11 Nov 2005) Fix deleting of all contours.
- (11 Nov 2005) Prevent crash if reconstructon from contours fails.
- (11 Nov 2005) Correct display of contours on oblique volume
slices.
- (11 Nov 2005) Correct filtering of contour cells on Spec File
Dialog.
- (10 Nov 2005) Fix editing of segmentation and paint volumes when
"ALL" slices are viewed in the main window.
- (9 Nov 2005) Add AC-PC
alignment to Edit Volume Attributes dialog.
- (8 Nov 2005) Add adjustable sampling for oblique volume slice
viewing to Display Control's Volume Settings page.
- (8 Nov 2005) Add contour and contour cell files to the list of
available transform data files.
- (7 Nov 2005) Change error message when orienting a surface so
that a paint named set of nodes is oriented away from the user.
This primarily occurs if the user is trying to flatten a partial
hemisphere and the CUT.FACE nodes are not identified.
- (1 Nov 2005) Fixed bug with deformation file naming that occurred
if the output spec file listed in the deformation map contained a path.
- (1 Nov 2005) Fixed bug with deformation of a coordinate file that
occurred if the topology file could not be read.
- (25 Oct 2005) In full hemisphere flattening, moved straggler tile
removal to prior to pushing the sphere flat. This corrects a
problem with a node along surface edge being dragged to the origin.
- (24 Oct 2005) Use only selected shape columns for surface shape
cluster analysis report.
- (24 Oct 2005) Contour alignment and MDplot import fixes.
- (12 Oct 2005) Multi-Fiducial Mapper - Fixed anomoly that if only
mapping to the averaged coord file, the algorithm was still mapping to
all of the individual cases.
- (12 Oct 2005) On Spec File Dialog, change the Select All and
Deselect All push buttons so that they only select or deselect files
that are currently shown using the file display filter toolbar buttons.
- (11 Oct 2005) Fix zooming of oblique volume slices.
- (11 Oct 2005) When in view mode and a transformation axis is
selected, avoid performing any ID Node or Voxel operations.
- (10 Oct 2005) Add metric deformation (nearest node or average of
nodes) to Apply Deformation Dialog.
- (10 Oct 2005) Corrected numerics on metric palette color bar when
user scale is selected with the positive or negative minimum not eqaul
to zero.
- (07 Oct 2005) Fixed problems with display of oblique volume
slices and transformation cells on the oblique slices.
- (06 Oct 2005) Add a Model Editor that allows the color of the VTK
Models to be changed. This coloring now includes opacity.
- (06 Oct 2005) Removed transformation matrix editor from the
Surface and Volume menus and placed it on the Window Menu.
- (06 Oct 2005) Add opacity to VTK models.
- (06 Oct 2005) Fix writing of VTK models in ascii format.
- (05 Oct 2005) Add Log base 2 to metric/shape/volume data
operations.
- (05 Oct 2005) Fixed bug in metric data deformation with tile
areas.
- (05 Oct 2005) Change toolbar's model selection control so that it
when VOLUME is in it, it also lists the label/filename of the bottom
most volume file.
- (04 Oct 2005) Fix problem with Spec File Dialog buttons sometimes
cutoff the bottom of the dialog.
- (04 Oct 2005) Fixes for slices selection in volume oblique slice
views.
- (03 Oct 2005) Add import of MdPlot files.
- (30 Sep 2005) Add node identification to montage volume views.
- (30 Sep 2005) Fix centering of obliqe slices whose display is
controlled by a transformation matrix.
- (29 Sep 2005) Allow display of transform data files (cell/foci)
even if the associated matrix's axes are not enabled for display.
- (29 Sep 2005) Fix "Mutex" warning seen on MS Windows version of
Caret when using the GNU compiler.
- (29 Sep 2005) Add identification of transform data files (cell,
foci) on oblique volume views.
- (28 Sep 2005) Fix bug on transformation matrix dialog that turned
the signs of all scale values to negative if the user just set one to
negative.
- (28 Sep 2005) Add display of transform data files (cells and
foci) in volume oblique views.
- (27 Sep 2005) Add montage for oblique slice views.
- (27 Sep 2005) Now have only one Volume Oblique View Rotation
Matrix. By default, the oblique slice views use the oblique view
rotation matrix unless the user has selected a matrix from the
transformation matrix file. Integrate oblique view matrix with
the transformation matrix dialog. For oblique view slices, the
slices in the toolbar are offsets from the oblique viewing slices.
- (26 Sep 2005) Add 3D view to "ALL" view for oblique volume slices.
- (23 Sep 2005) Add "ALL" view for oblique volume slices.
- (22 Sep 2005) Add foci to oblique volume slice views.
- (21 Sep 2005) Add oblique volume slice X, Y, and Z views.
These slices are automatically yoked to the main windows Oblique
View. An option on the Display Control's Overlay/Underlay -
Volume's Settings panel allows the oblique slices to be yoked to a
transformation matrix.
- (19 Sep 2005) New Surface Vector
File. Add a vectors submenu to the attributes menu. The
only item on the Vectors submenu creates vectors based upon the
difference between two loaded surfaces.
- (15 Sep 2005) When drawing borders and assigning the nodes within
the borders, allow the border assignment to operate when drawing 3D
borders.
- (15 Sep 2005) Add square root to mathematical operations on
metric, shape, and volume data.
- (13 Sep 2005) Fixed crash when a focus was identified with only a
focus file was loaded and multiple fiducial surface files were loaded.
- (13 Sep 2005) Fixed crash when an ID was performed in main window
immediately after a viewing window was closed.
- (13 Sep 2005) Remove use of size in cell/foci file when drawing
cells/foci (see 12 Sep 2005).
- (12 Sep 2005) If a voxel is indentified on a volume viewed
obliquely, use the oblique rotation matrix to determine the voxels
coordinates.
- (12 Sep 2005) Allow the user to identify multiple nodes by having
the user places spaces between the node numbers.
- (12 Sep 2005) Use size from cell/foci file when drawing
cells/foci.
- (09 Sep 2005) Fix bug with selection of loaded volumes for volume
to surface mapping.
- (09 Sep 2005) Add operation to
Surface Region Of Interest Dialog that automatically draws borders
around clusters of selected nodes.
- (08 Sep 2005) Add "ring" symbol for cells and foci. On
Display Control Dialog, allow user to override the color file symbol
for cells and foci.
- (07 Sep 2005) Fix display of foci diamond symbols on flat
surfaces.
- (07 Sep 2005) Change surface to volume process by replacing
"thickness" with an inner and outer boundary.
- (07 Sep 2005) Add "Validate Spec File" to the File Menu.
This queries the user for the name of a spec file and then verifies
that the spec file and its data files exist. Copy Spec File and
Zip Spec File now validate input spec file.
- (06 Sep 2005) Surface Region of Interest Paint Subregion Report:
Add center of gravity for regions X/Y/Z/Lat/Long coordinates.
- (06 Sep 2005) Add item to file
menu that "zips" a spec file and its data files. In addition, the
same functionality is provided by the new command line program
"caret_zip_spec".
- (02 Sep 2005) Pressing on
CTRL-Esc(ape) key combination on a window will pop up a file dialog for
saving an image of the window.
- (01 Sep 2005) Fix reading of MINC volumes whose data is not
stored in an LPI orientation (zspace, yspace, xspace).
- (31 August 2005) When drawing a border and assigning the nodes
within the closed border to a new column, make the newly created paint
column the selected paint column on the draw border dialog.
- Change version to 5.31.
- (31 August 2005) For brain models, separate view scaling into X,
Y, and Z components.
- (31 August 2005) Add some tooltips to the Transformation Matrix
Editor Dialog.
- (30 August 2005) Increase width of scale spin boxes on graph
widget (used by SureFit operation's gray and white peak histogram
panel).
- (30 August 2005) Add button on Transformation Matrix Dialog to
set the matrix's translation by clicking the mouse on a object.
- (29 August 2005) Fix some problems with rotation of
transformation matrix axes in screen space.
- (10 August 2005) Add button to Map Stereotaxic Focus Dialog
Studies panel for deleting the selected study.
- (09 August 2005) Replace graph on the SureFit Segmentation Dialog
with a new and improved graph for histogram display.
- (09 August 2005) Correct histogram dialog on SureFit Segmentation
Dialog so that is lists the actual voxel values and not the voxels
scaled 0 to 255.
- (09 August 2005) Add high (original) and low thresholding for
removal of hindbrain during SureFit Segmentation.
- (08 August 2005) Fixed crashing of SureFit Segmentation algorithm
if the eye and/or hindbrain removal is skipped. Fixed auto-saving
of surface files when inflated type surfaces are not generated.
- (05 August 2005) Add additional attributes for color files: alpha
channel and symbol type. Both alpha channel and symbol type are
used by cells and foci. With additions to ColorFile, write the
color files in XML format.
- (04 August 2005) Add Cell and
Foci Report that list attributes about cells/foci. In addition,
paint information for the node nearest to each cell/focus may also be
shown in the report.
- (03 August 2005) Add
mathematical operations to the command line program "caret_metric" used
to modify metric files at the command line.
- (02 August 2005) Fixed bug that failed to delete the intermediate
files created during the deformation process.
- (02 August 2005) Bug fix for surface deformation. If a data
file failed to deform, the deformation immediately terminated and no
more data files were deformed. Now, if a data file fails to
deform, the deformation process stores the error message and continues
with the deformation process. After the deformation process has
completed, error messages involving problems with deformation of data
files are displayed.
- (02 August 2005) Add cells and foci for display on volume slices.
- (01 August 2005) Attributes:Metric:Convert Metric Column to
Functional Volume: Now have two options to interpolate (the existing
functionality) or largest neighbor which sets the voxel to the larget
metric value of the nodes that intersect the voxel.
- (29 July 2005) Add "oblique"
volume viewing. Include ability to yoke a surface in a viewing
window to the volume for assisting with oblique volume orientation.
- (28 July 2005) Draw Border Dialog: disable paint assignment if
the 3D selection is set.
- (28 July 2005) Edit Volume Attributes Dialog: add buttons for
setting the Parameters File's AC or Whole Volume AC using the origin
and voxel size.
- (28 July 2005) Volume Resize Dialog: add option (defaulted on)
for updating the Params File X/Y/Z min with the minimum cropping values.
- (27 July 2005) If loading a cell/foci or cell/foci projection
file and choosing to replace, delete cells/foci of all types.
- (27 July 2005) Allow saving of cells for any surface type.
- (27 July 2005) On reconstruct volume into
Volume:Segmentation:Reconstruct Into Surface Dialog, add option to
create a hypersmoothed surface.
- (27 July 2005) Add new StereotaxicSpace class and use for all
dealings with stereotaxic spaces.
- (26 July 2005) Update Map Stereotaxic Focus Dialog that is split
into two tabs for "Focus" and "Studies". Add additional GUI
components for new foci data items. Also, add button for deleting
the selected focus.
- (25 July 2005) Add additional data to cell/foci files and
cell/foci projection files all of which are now written in XML format.
- (22 July 2005) Move common items from CellData class and
CellProjection class into new parent class CellBase.
- (21 July 2005) Allow user to set the random number generators
seed value. If not set by user, default seed to the number of
seconds since 1970.
- (20 July 2005) When applying a transformation to a volume, allow
the volume dimensions to grow so that the volume data does not get
cropped.
- (20 July 2005) Fixes/enhancements for volume transformations.
- (20 July 2005) Fix but in new histogram dialog (14 July 2005) and
add an Apply button for graph scale axes.
- (20 July 2005) Fix colors for cuts during flattening of monkey
brains but updating template borders with name of color file.
- (20 July 2005) When a data file is saved with its name being
changed, properly keep track of loaded files for scene creation and
loading.
- (19 July 2005) For entering foci, convert "em" or "en" dash
characters (characters with varying length dashes, unicode charcters
8208 to 8213) to hyphens (minus signs).
- (18 July 2005) Fix memory leak in VolumeFile operator=() that
caused Caret to run out of memory during automatic error correction.
- (18 July 2005) Fix up display of default gray/white peak
histogram on SureFit Segmentation Dialog.
- (18 July 2005) Consolidate histogram selection combo boxes
scattered about into a single component.
- (14 July 2005) Replace histogram dialog with a much improved
version that allows complete control of the axes' scale and a grid
background.
- (13 July 2005) Change
computation of standard deviation so that "N-1" is used for division in
the formula. This implies that the true mean is unknown and that
the data is a sample from the population.
- (12 July 2005) Fix yoking so that if the surface is changed in a
viewing window, yoking remains selected.
- (12 July 2005) For surface shape cluster analysis on ROI dialog,
warn user if no metric column is available for distortion correction.
- (12 July 2005) Add "MFM" to multi-fiducial mapping statisitical
measurement column names.
- (12 July 2005) Fixed bug that caused a crash if a volume file was
loaded and the metric cluster and smoothing dialog was displayed.
- (11 July 2005) Fix bug in Surface: Region of Interest: Surface
Shape Cluster Analysis. Any previously run cluster analyses are
probably incorrect.
- (07 July 2005) For Attributes Menu Compute Mean and Deviation on
Metric/Shape, allow user to choose what should be computed and set the
column names.
- (07 July 2005) When switching from a flat surface with rotation
axis set to OFF to a non-flat surface, default the rotation to XY.
- (07 July 2005) Default Reference Column on Surface ROI: Surface
Shape Correlation Report to ALL.
- (06 July 2005) Change Attributes:Surface Shape:Subtract Group
Average on Shape Files so that it operates on two surface shape files.
- (06 July 2005) Fixed bug that occurred when the Surface Region of
Interest Dialog was open and the number of metric, paint, or shape
columns was reduced.
- (06 July 2005) Add more text about shape file to Surface Region
of Interest text report.
- (06 July 2005) Add option on Attributes:Surface Shape menu to
normalize all columns in a surface shape file.
- (06 July 2005) For Attributes:Surface Shape: Compute T Map
Shuffled Column, default coloring mapping to +/- 5.0.
- (05 July 2005) Add fitting of metric or surface shape column data
to a normal distribution.
- (05 July 2005) Fix crash that happened when loading a topography
file.
- (01 July 2005) Add Vector
Volumes which store a volume of vectors as a 4 component volume with
the first three components being the unit vector and the last component
being the magnitude.
- (29 June 2005) Allow events to process during SureFit Error
Correction.
- (28 June 2005) For SureFit operations, if generating a
segmentation and performing error correction, generate a surface from
the initial segmentation and display it so that user can verify that
there are no major problems such as the skull hanging around.
- (28 June 2005) Fix near to planes in volume script builder.
- (28 June 2005) Add surface shape cluster report to surface region
of interest operations.
- (27 June 2005) Fix 3D border drawing.
- (27 June 2005) Correct application of a transformation matrix to
a volume.
- (26 June 2005) Add a few annotations to the Display Control
Dialog.
- (26 June 2005) Make dialog that shows errors encountered while
checking all scenes non-modal.
- (26 June 2005) Change warning message when unloading all files
but scene and spec and there are modified data files.
- (26 June 2005) Enable a vector file to be written as text.
- (26 June 2005) When reporting foci stereotaxic position, always
report the position on the active fiducial surface.
- (26 June 2005) For scenes, retain the topology file assigned to
each of the displayed surfaces.
- (23 June 2005) Fix scene check bug for deleted surfaces still
appearing to be present.
- (23 June 2005) Add computation of Z-maps and T-maps for surface
shape files.
- (22 June 2005) Allow cells and foci drawn as sphere to have a
size less than 1.0.
- (21 June 2005) Set all volume coloring invalid when scene changed.
- (21 June 2005) When checking scenes, verify that all needed files
are in the Spec File.
NOTE: Remaining changes are listed from oldest to newest.
04 April 2004 - Release version 5.1
- (12 April) Version changed to 5.11.
- (12 April) Changed flat multi-resolution morphing parameters.
- (12 April) Fixed spherical registration borders (dorsal medial
wall, ventral medial wall, and calcarine) produced during full
hemisphere flattening.
- (12 April) Generate latitude longitude borders so that the north
pole is at the lateral pole which is the tip of the Central
Sulcus.
- (12 April) Assign border colors after generating cartesian grid
or lat/lon borders.
- (12 April) If no paint or area color file was provided at start
of flatten full hemisphere, the paint and area color file names ended
up like "paint_file_#" and "color_file_#". Now uses topo file
name to get a file name prefix for paint and area color files.
- (12 April) If borders are loaded and border display is off, turn
on display of borders.
- (12 April) Add option to Save Data File Dialog to remove
duplicate borders/border projections when saving a border or border
projection file.
- (12 April) Add menu item to rename a border by clicking on it
with the mouse, which pops up a dialog allowing the border to be
renamed.
- (13 April) Remove some static data from node coloring.
- (14 April) When performing multi-resolution morphing, only add
the last coordinate file to the spec file. Other cycles are still
saved, just not added to the spec file.
- (14 April) Use meaningful names for spherical lat/long borders.
- (14 April) Move unrecognized spec file tags to the spec file's
header.
- (14 April) Default border saving so that it removes duplicate
borders.
- (14 April) Spec File Dialog change to the remove from spec file
"X" button next to each file. Now when the user presses the "X",
the line is grayed out. If the user presses the "X" again, the
line is re-enabled so that the file is not deleted. If a line is
grayed out when the spec file dialog closes, the file is removed from
the spec file.
- (14 April) Add binary format
for coordinate and topology files.
- (15 April) Add binary format
for areal estimation, lat/lon,
metric, paint, rgb paint, section, and surface shape files.
- (16 April) Replace current normals calculation that uses VTK
because it is slow. Replace with normals calculation using
coordinates and
topology.
- (16 April) Do not classify nodes after reading a spec file.
Instead classify as needed such as when the primary overlay is
set to Edges or the surface is drawn with Links-Edges only.
- (16 April) Add utility program "caret_file_convert" to convert
between binary and text (ascii) files.
- (16 April) Add computation of average and deviation for each node
in the surface shape file.
- (19 April) Enable multi-threading for multi-resolution morphing.
- (20 April) Add a copy button to the Identify dialog to copy the
highlighted text to the clipboard.
- (21 April) Update all projected files when surfaces are aligned.
- (21 April) Add option to expand or shrink a surface along the
surface normals to Surface: Geometry menu.
- (21 April) Fixed bug that prevented fast open data file dialog
close button from closing the dialog when the auto close checkbox was
unchecked.
- (21 April) Add a second light opposite of the existing light when
drawing functional volume voxels so that they do not appear dark gray
in the dorsal view.
- (22 April) Add additional functional volume mapping algorithms
for mapping functional data within Caret.
- (26 April) Default to new column each time a functional volume is
mapped within Caret.
- (27 April) Do not allow spec file name to be changed in
map_fmri_to_surface on the metric naming dialog.
- (28 April) Created new program "caret_metric" for performing
clustering and smoothing of metric files at the command line.
- (29 April) Created deformation map file version 2. In this
version, two new items are added, the source (individual) and target
(atlas) directories. All of the source and target files are
written relative to these directories. When applying a
deformation map, the source and target directory names are verified to
see if they exist. If not, the user must set them. This
change simplifies the movement of a
deformation to another computer system.
- (29 April) map_fmri_to_surface so that it will display an error
message if the atlas surface directory file (typically named
"map_fmri_atlas.directory) version is 2 or greater.
map_fmri_to_surface will be replaced with a program named
"caret_map_fmri".
- (29 April) Correct problem with every other frame being black
when recording animation through volume slices.
- (29 April) Fixed origin of AFNI volumes stored with R-A-S
orientations. It was off by one voxel.
- (30 April) Modify caret_file_convert to convert FreeSurfer
Surface, Patch, Curvature, and Functional files to Caret format.
Also convert VTK polydata.
- (3 May) Rewrite some of caret_file_convert. Add BYU and STL
file conversion.
- (5 May) Add option on Display Control Dialog's border panel for
adjusting the stretch factor when borders are draw as unstretched lines
on a flat surface.
- (5 May) Attributes: Lat/Long: Generate Lat/Long on Spherical
Surface now assumes that the default view of the sphere is a dorsal
view. Positive latititude is along the lateral axis and negative
latitude is along the medial axis.
- (7 May) Fixed problem with metric smoothing algorithm.
- (7 May) Added Clustering and
Smoothing for Surface Shape files.
- (7 May) Fixed bug with caret_metric program crashing on Linux.
- (11 May) Initial implementation of new fMRI mapper for individual
and a surface loaded within Caret.
- (11 May) Add "?" button for RGB paint on Display Control Dialog.
- (11 May) Add display of surface shape information in the Identify
Dialog.
- (11 May) Add reference surface and surface used during distortion
calculations to the surface shape
column comments.
- (11 May) Add the name of the surface used for curvature
calculation to surface shape column comment.
- (11 May) Fixed problems on histogram dialog when viewing middle
96%.
- (11 May) Add button to set all columns to do not load when
loading a node attribute file such as
paint.
- (11 May) Add option at Caret5 startup "-loadspec
<spec-file-name>" that automatically loads the data files
contained in "spec-file-name" into Caret. The option "-spec
<spec-file-name>" simply loads the spec file "spec-file-name"
into the
spec file dialog.
- (12 May) Added Mathematical
Operations to Attributes: Metric and
Attributes: Surface Shape. This allows two columns to be
added,
one column to be subtracted from another, one column to be divided by
another, two
columns to be multiplied, a column to be multiplied by a scalar, and a
scalar added to a column.
- (12 May) Add standard error for metric and shape average and
standard deviation computation.
- (12 May) Fixed some problems with probabilistic atlas coloring.
- (12 May) Bug fix on D/C panel for prob atlas letting previous
page show thru.
- (12 May) Split metric clustering threshold into negative and
positive.
- (13 May) Now able to save (projected) foci associated with each
surface type. However, only fiducial foci files are added to the
spec file can Caret still only loads
foci associated with the fiducial surface.
- (14 May) Fixed cell/foci projection problem. When
cells/foci project inside a tile, the offset of the cell or focus from
the tile is saved as a vector in relation to the fiducial surface.
The problem is that a cell or focus around the inferior part of
the fiducial surface may have a vector with a negative z component.
When this cell or focus is unprojected on the flat surface, it
ends up under the flat surface when it really should be above the flat
surface due to the offset vectors negative z component. Now, the
signed distance to the surface is combined with the surface's tile
normal to properly offset the cell or focus when unprojecting.
- (17 May) Default registration border resampling to 10.
- (17 May) When deforming node attribute files, column names are
prefixed with "deformed". File comments now include name of
source file being deformed and the name of the deformation map file.
- (18 May) Default probabilistic atlas to "normal" display.
- (18 May) Add editing of surface shape column names to display
control dialog.
- (18 May) Fix editing of metric column names so that main display
control page gets updated.
- (19 May) Add option on save data file dialog to inhibit the
automatic appending of a file type extension to the file's name.
- (19 May) Add button to volume attributes editor dialog to use the
params file AC to set the volume's origin.
- (19 May) Add display of params file data in the "names" tab of
the view data file comment dialog accessed by pushing the "?" button on
the View Data Files or the Spec File dialogs.
- (19 May) Add to Surface Region
of Interest Dialog. New
query that determines correlation coefficients between one column of
surface shape and all other surface
shape columns.
- (20 May) Add item to Surface:Topology Menu to use
vtkPolyDataNormals to consistently orient the triangles in the surface
topology.
- (21 May) Fixed error in metric and shape statistics that snuck in
when standard error was added on 12 May.
- (24 May) Add option to display a surface shape color bar in
graphics windows.
- (24 May) Do not require spec files when applying a deformation
map to deform a data file.
- (24 May) Add "deformed with" to columns when deforming a node
attribute data file.
- (24 May) Add check in spherical deformation for border files that
are projected to nodes at origin.
- (24 May) Add spin boxes to color selection dialogs.
- (28 May) Add Layers:Borders:Create Average Borders to create
average borders form border files that contain borders with the same
names.
- (1
Jun) Update Macaque flatten hemisphere template borders with
http://brainmap.wustl.edu:8081/sums/archivelist.do?archive_id=3370597.
- (1
Jun) Use MIstart and MIstop parameters as origin and voxel size when
importing minc volumes.
- (2 Jun) Modify surface region of interest surface shape
correlation report to enable correlation between all columns (creates
NxN matrix).
- (7 Jun) Add "version_id" to header each time a file is written.
These version_id's will by used by SuMS to keep track of a files
"heritage".
- (10 Jun) In identify dialog, show coordinates for all open
windows with surfaces displayed.
- (10 Jun) Create a deformation field when a spherical deformation
field is computed. This currently only compute the individual's
deformation field.
- (11 Jun) Add Generate Deformation Field to the Attributes Menu
and display deformation fields as a layer controlled through the
Display Control Dialog.
- (14 Jun) Compute normals as first step when computing surface
curvature.
- (14 Jun) Add optional perspective projection.
- (15 Jun) Reduced time to make surface cuts.
- (22 Jun) Create atlas deformation field when performing a
spherical registration or, post deformation, using the Attributes Menu.
- (22 Jun) Add ability to deform
coordinate files so that multiple
cases may be loaded and viewed simultaneously in a single Caret session.
- (23 Jun) Add information to Smoothing Dialog to inform the user
that normals should be regenerated after smoothing a surface.
- (23 Jun) Add Dialog to Surface Menu for averaging coordinate
files.
- (23 Jun) Add name of deformation map file to deformed coordinate
file.
- (24 Jun)
Increase total number of model windows from 5 to 10.
- (25 Jun) Fixed error that gave a paint file created during
flattening of a full hemisphere an area color file extension. Add
a check at the beginning of flattening a full hemisphere for a paint
file.
- (25 Jun) Limit update of version_id in spec file to once per
caret session when saving data files.
- (28 Jun) Add creation of topology file when deforming a flat
coordinate file.
- (28 Jun) Add warning when saving a volume in AFNI format and the
file name does not end in an extension like "+tlrc.HEAD".
- (30 Jun) Create binary version of deformation map file.
- (30 Jun) Fixed bug with using a pre-loaded border file for
template cuts when flattening a full hemisphere. Users must now
use an ellipsoidal border file.
- (1 Jul) Add Copy Spec File to
File Menu for copying spec files.
- (2 Jul) Added an interface to
the SuMS database for downloading
and uploading data sets. This is selectable from the Comm Menu.
- (2 Jul) Add option (defaulted on) to the Flatten Hemisphere
Dialog to smooth the medial wall of a fiducial surface during
flattening of the full hemisphere.
- (2 Jul) Add Convert Data Files
Format to File Menu to convert
data files between text and binary format.
- (6 Jul) Trim leading and trailing whitespace when reading data
file tag/value pairs.
- (7 Jul) Implement surface editing (Surface:Edit menu).
- (7 Jul) Possible fix for clipping problems seen in Surface &
Volume mode. When optional perspective view was added, a call to
gluLookAt() was also added but was being called for both perspective
and orthographic viewing modes.
- (7 Jul) Fixed crash after import of free surfer surface due to
colors not being assigned.
- (8 Jul) When uploading a spec file to SumsDB, strip the path from
all of the data files listed in the spec file.
- (8 Jul) Limit number of version_id updates to just one when a
file is written out multiple times in a caret session.
- (8 Jul) Add selection of previous data file directories on open,
save, import, and export file selection dialogs.
- (8 Jul) Clear file data file names on deformation dialog when a
spec file is selected.
- (9 Jul) No longer set version_id in file header when a data file
is written. version_id will now be updated by SumsDB.
- (9 Jul) Added volume borders.
- (22 Jul) Implemented new
functional volume to surface mapper.
Removed "map_fmri_to_surface" from attributes:metric menu.
"caret_map_fmri" is now command line only.
- (22 Jul) Limit width of parameters (space, species, hem, etc) on
spec file dialog so that all are visible even if data files have very
long names making dialog very wide.
- (23 Jul) Add quick mapping of a functional volume to an atlas
surface to the Volume:Functional Menu.
- (26 Jul) Fix crash
if a coordinate file is read without any other files
having been read.
- (26 Jul) Limit width of previous spec files on choose spec file
dialog.
- (26 Jul) Limit width of previous directories on open and save
data file,
and import and export file dialogs.
- (27 Jul) Added a spin box on the right side of the Identify
Window to control the number of digits to the right of the decimal
point in
the data display window.
- (27 Jul) Add "All On" and "All Off" buttons to surface region of
interest attributes page.
- (27 Jul) When reading a coord file, check its header for the
topology file used by the coord file when the coord file was last
saved, and, if that topology file is loaded, assign the topology file
to the coord file's surface.
- (27 Jul) Add brain model selection to the popup menu.
- (27 Jul) Add menu item on Layers:Borders menu to convert volume
borders into fiducial cells.
- (28 Jul) Moved active fiducial surface (used in surface &
volume and for
overlay on volume) from Surface Information Dialog to Display Control
Dialog's Surface Miscellaneous panel.
- (28 Jul) Combo box at top of Display Control Dialog now only
lists pages
for data that is loaded.
- (28 Jul) Holding down the CNTRL key (Apple on Macs) and pressing
F1, F2,
..., F15 over a caret window will switch to the surfaces and
volumes as listed in the toolbar's model selection menu.
- (28 Jul) Store and use hem_flag
in coord file header so that
different hemispheres may be loaded simultaneously and toolbar buttons
will work correctly.
- (29 Jul) Add ability to set the maximum and minimum values
for metric or surface shape on the metric/surface shape dialog.
- (29 Jul) Add volume
mathematics.
- (29 Jul) Add optional output file parameter for "caret_metric"
command line program.
- (29 Jul) Add import of raw volume files.
- (2 Aug) Add independent surface
coloring that allows each surface
to have its
own surface coloring.
- (2 Aug) Add ability to set hemisphere for a surface from the
surface information dialog.
- (3 Aug) Change independent surface coloring on display control
dialog so that the control is available on all sub-pages that deal with
surface attributes.
- (3 Aug) Fixed "New Spec" button on spec file dialog so that it
creates a spec file with all selected files.
- (3 Aug) When using "New Spec" button and the user selects an
existing spec file, give the user the opportunity to overwrite or
cancel.
- (5 Aug) Added display lists for
surface drawing.
Significantly improves performance on Macs.
- (5 Aug) Fixed bug that
voxels were not colored on surface and volume if a volume
was not previously viewed.
- (5 Aug) Add ability to
draw segmentation volume voxels as filled, open squares,
or crosses.
- (6 Aug) Add ability to
specify type of ouput file (binary or text) produced
by the program "caret_metric".
- (10 Aug) Add "caret_sphere_deform", a command line program for
performing spherical registration.
- (11 Aug) Add experimental
smoothing that uses curvature and normals from an equation
in a "level sets" paper. It can produce a surface similar to the
inflated surface but with some high frequency spikes.
- (13 Aug) Add graph that pops up
when a node is identified, a
metric is underlay or overlay, and popup graph is selected on metric
panel of overlay underlay dialog.
- (27 Aug) Fix bug that caused a blank image when the main window
was saved as an image with display lists on.
- (30 Aug) Add a "Simplify Surface" item to the Surface menu to
reduce the number of polygons (and nodes) in a surface.
- (31 Aug) When a volume file is read, default its sub-volume name
to the name of the volume. If there is a sub-volume name in the
volume file's header it will override the default name.
- (31 Aug) Add segmentation volume editing - erosion and dilation.
- (31 Aug) Default display lists
off if the OpenGL library is a "Mesa" OpenGL library.
- (1 Sep) Change "Finish" button
on Map Fmri Dialog to "Map Data".
- (1 Sep) On Map Fmri Dialog, only clear mapping surfaces if a
volume is added or deleted.
Previously, the mapping surfaces were removed when the
volumes page was displayed.
- (1 Sep) Remove Copy/Download Spec File page from Map Fmri Dialog.
- (1 Sep) Modify Map Fmri Dialog
so that average is created for each volume and multiple surface set.
- (2 Sep) Modify Draw Border Dialog so that it checks for rotation
when the Apply button is pressed on the Draw Border Dialog if a flat or
compressed medial wall
surface is being viewed. If there is a rotation, the warning will
be displayed allowing the user to remove the rotation or ignore
it.
- (2 Sep) When processing the mouse allow no mouse movement or a
very tiny mouse movement to
preform and ID node operation when in View Mode.
- (2 Sep) When computing metric/shape avg/dev/error, default the
color mapping to the min and
max values in the respective columns.
- (2 Sep) Add segmentation volume
editing flood fill and remove connected region.
- (2 Sep) Add ability to set metrics or surface shape for nodes in
an ROI.
- (2 Sep) Modify color file editor to that when creating a new
color, the name of the new color and its attributes are the same as the
currently selected color.
- (3 Sep) Add ability to adjust threshold for probabilistic atlas
threshold display.
- (3 Sep) Add new Attributes:Probabilistic Atlas menu item for
converting a currently selected as overlay/underlay threshold
probabilistic atlas to a paint column.
- (3 Sep) Add hemisphere to parameters on file save dialog when
saving a coordinate file.
- (7 Sep) Modify volume animation. Now start on currently
viewed slice. Have ability to set animate direction (positive or
negative slice increment) and can set direction while paused.
- (7 Sep) Fixed bug that caused a functional volume to be
incorrectly colored when there was no metric file loaded. This
probably resulted when independent surface coloring was added.
- (8 Sep) Added Wu Region File
that
when used with a ROI volume (paint volume), a graph will popup
when a node is identified that is in a selected ROI showing the
timecourse for the region.
- (9 Sep) Add dialog on attributes paint menu to map a paint volume
into a paint file column.
- (9 Sep) Changed code for updating
GUI due to data file changes to allow for more than 32 files.
- (9 Sep) Add import of SUMA's RGB file.
- (10 Sep) fMRI mapper - change name
to "AVERAGE - volume-name" and include names of coordinate
files in the average column's comment.
- (10 Sep) Add ability to set the column names for lat/lon file
columns.
- (10 Sep) Add ability to selectively read columns from a lat/lon
file.
- (10 Sep) Display lat lon column names in ID window.
- (10 Sep) Modify Create Average Coordinate file so that a surface
shape file containing the standard deviation for each node in relation
to the surfaces it was averaged from.
- (10 Sep) Add ability to use a
surface shape column as a node
position uncertainty that can be enabled on the Display Control
Dialog's Surface Shape panel.
- (13 Sep) Separate gaussian computation from Metric Mapping into
it own class. Add gaussian smoothing to metric smoothing for both
caret and command line metric smoothing.
- (13 Sep) Add option on Open Data File dialog to indicate than an
SPM2 volume is being read that has the right on the left.
- (14 Sep) Modify spherical registration so that it deforms
individual coordinate files to the atlas.
- (15 Sep) Completed geodesic
distance
so that a path may now be displayed from the root node to the
identified node. Geodesic data may now be saved to a
geodesic distance file including multiple geodesic queries.
Display of geodesic data is controlled on the Display Control's
Geodesic
panel.
- (15 Sep) Add spherical coord files to the indiv coord files that
will be deformed to the atlas when a spherical deformation is run.
- (15 Sep) When a flat surface is selected for display, disable
surface rotation. It may be re-enabled by selecting the rotation
axis in the toolbar.
- (20 Sep) Modify region graph to allow all time courses for
display.
- (21 Sep) Change spin box for Inflate Surface Dialog's
inflation factor to step by 0.01 instead of
0.1.
- (21 Sep) Add new palette file editor on Attributes:Palette Menu.
- (22 Sep) Fixed problem with floating point spin box on surface
inflation dialog by replacing floats with double in the floating point
spin box widget.
- (22 Sep) Misc changes to fMRI mapper.
- (27 Sep) If edges only is display mode,
do not allow selection of non-edge nodes.
- (28 Sep) Do not put "Sub Volume" in volume file sub volume names.
- (28 Sep) When a spec file is read, determing volume data files
for any volume names that are specified with only the volume's header
file.
- (28 Sep) Update SuMS interface for host
"sumsdb" instead of "brainmap".
- (04 Oct) Make column names longer for metric, paint, shape on
Display Control Dialog.
- (04 Oct) Show beginning of names when Opening a Node Attribute
Data file and choosing columns for loading.
- (04 Oct) Add new Surface ROI - Statistical Report on Paint
Subregions which performs a statistical report for each unique paint
name in a selected paint column.
- (04 Oct) Add option to Display
Control Dialog to select a paint
column which is checked for MEDIAL.WALL. If it has medial
wall
paint, and the option is enabled, the medial wall is colored overriding
any and all overlay/underlay selections.
- (8 Oct) Add path to spec file name when starting caret and
loading a spec file (ie: caret5 -loadspec brain.spec) so that the spec
file may be successfully opened using File:Recent Spec File.
- (11 Oct) Separate OpenGL code from graphical user interface so
that it can be used by WebCaret.
- (11 Oct) Fixed problem with changing border color line size.
- (11 Oct) Fixed bug with copying spec file that caused files to
disappear if both the new and copied spec file were in the same
directory.
- (12 Oct) Create a default set of sections
(1mm Y-axis) when a brain set is loaded that contains a fiducial
surface.
- (12 Oct) Fixed bug for display of sections (needed to delete
display lists).
- (12 Oct) Fixed bug for display of ROI highlighted nodes.
- (12 Oct) Moved some code involving node display flags from
BrainModelOpenGL to BrainSet and BrainSetNodeAttribute for better
WebCaret compatibility.
- (12 Oct) Fixed bug in Metric & Surface Shape file that was
requesting way to much memory.
- (13 Oct) Add gaussian smoothing for metric
data that uses a spherical surface for some distance cutoffs.
Updated caret_metric.
- (13 Oct) Fixes for after contour and volume reconstruction.
- (14 Oct) If a viewing window is open, show
the name of its brain model in the window menu.
- (14 Oct) Replace icon on standard dialogs with the caret icon.
- (14 Oct) Fix text for metric color palette
bar. Skip QFont code in BrainModelOpenGL for WebCaret.
- (14 Oct) Add volume resampling by entering
the desired voxel sizes.
- (14 Oct) If a file is not found, prepend "(FILE NOT FOUND)" to
its name on the spec file dialog.
- (14 Oct) Add spherical retessellation on Surface:Topology menu
when caret is started with the flag "-test".
- (15 Oct) Add display of euler count on surface information dialog.
- (15 Oct) Add SID button on Identify Dialog
to inhibit the display of green symbols on the surface.
- (15 Oct) Add display control of volume crosshairs to Display
Control Dialog's Overlay/Underlay Volume page.
- (15 Oct) Add anatomy volume thresholding (green above upper
threshold, blue below lower threshold) to the Anatomy Histogram
available on the Display Control Dialog's Overlay/Underlay Volume page.
- (15 Oct) Fix import of SUMA RGB file with color components
ranging 0.0 to 1.0.
- (18 Oct) Add rotation to volume
display and
ability to apply the rotation to the displayed volumes.
Also
added ability to apply a transformation matrix volume files.
- (18 Oct) Fix RGB coloring when it is the underlay to not allow
anything to show through.
- (18 Oct) Add continuous rotation to the Automatic Rotation dialog.
- (20 Oct) Add Dialog for editing parameters file.
- (29 Oct) Fixed crash that occurred if the Map Functional Volumes
to Metric dialog was selected and at least one brain model other than a
surface was loaded.
- (29 Oct) Remove splash image and show surface after loading a
spec file (bug fix).
- (29 Oct) "Show Surface" pushbutton on Display Control's Surface
and Volume panel had no effect when display lists were enabled (bug
fix).
- (01 Nov) After loading a volume file, do not check to see if all
voxels are less than one and delay color assignment until the first
volume is loaded.
- (02 Nov) Only allow volume rotations when the "Rotation
Enabled" item on the Volume:Transform menu is checked.
- (02 Nov) Fix uploading of volume files so that
the header AND the data are uploaded when only the header is selected.
- (03 Nov) Fix crash if a spec file loaded with a coord file and no
or invalid topology file.
- (03 Nov) Restored lost functionality that displays a cross over
the surface in other windows when a node is identified or a voxel is
identified.
- (03 Nov) Modify gaussian function so that it is now exp(x*x /
2*sigma*sigma). Previously "2" was not in denominator.
- (16 Nov) Replace VolumeFile with a version that
does not use VTK to store the volume data.
- (16 Nov) Enable Map to Caret With Atlas when any surface is
loaded and atlases are available.
- (17 Nov) Add ability to segment an anatomical volume, produce a
segmentation volume, and generate raw and fiducial surfaces.
- (17 Nov) Improve 3D border
drawing by determining the triangle
under the cursor and using the barycentric position
in the triangle to place the border point. Previously the
border
points were pulled to the nearest node.
- (18 Nov) Allow update of comments in volume files on disk through
the Open Data File dialog.
- (18 Nov) Change "New Spec" button on Spec File Diaog to "Create
New Spec" and warn user if choosing an existing spec file name.
- (18 Nov) Fixes for Convert Data Files Dialog. Had two "Add
Files" button and one of them should have been "Remove Files".
Also remove all files when Close button is selected.
- (18 Nov) When reading a segmentation volume assume any non-zero
voxel is part of the segmentation and changes its value to 255.
- (18 Nov) Add translucent display of segmentation volumes.
- (19 Nov) Add ability to combine two paint volume files using
Volume:Mathematical Operations Dialog and choosing to combine
paint volumes.
- (22 Nov) Add Probabilistic Atlas Analysis to Surface Region of
Interest Dialog.
- (22 Nov) Fix glitch with display of threshold probabilistic atlas.
- (22 Nov) Add adjustable transparency for segmentation volume.
- (22 Nov) Add ability to set name of output volume on volume
mathematics dialog.
- (22 Nov) Add ability to write volume brick files gzipped.
- (22 Nov) Add ability to read/write paint volumes from/to AFNI
volume files.
- (23 Nov) Fix bug that caused part of the surface to be clipped at
times. This would only happen after a volume had been viewed and
the user switched back to viewing a surface. When a volume was
drawn, it was overriding the near and far clipping planes.
- (23 Nov) Speed up surface coloring by applying coloring from
first surface to all other surfaces with the same color selections.
- (24 Nov) Add ability to save
all volumes of a specified type
(anatomy, paint, etc) to a single multi-volume AFNI file.
- (29 Nov) Fixed problem with deformed coordinate file being given
hemisphere "unknown" which causes standard view buttons in toolbar to
work incorrectly.
- (29 Nov) Fixed bug with a program error being printed regarding
an invalid display list when surface to volume conversions were
performed. Solution was to create an "operator=()" for
AbstractFile and prevent the display list number from being copied.
- (29 Nov) Provide more information on Save Data File Dialog when
saving an AFNI volume about proper file naming.
- (29 Nov) Creating batch deformation file, omit file parameters
that are blank.
- (29 Nov) During flattening of a full hemisphere, while creating
the landmarks for registration, remove the last link in the dorsal and
ventral medial wall landmarks so that they do not overlap. If
there is an overlap, it may cause crossovers during registration.
- (29 Nov) Fixed reading of version 0 topography files.
- (30 Nov) Added volume region of interest dialog with
probabilistic paint analysis query.
- (01 Dec) Additions to volume region of interest dialog.
Added selection by segmentation volume, thresholded anatomy
volume, and thresholded functional volume. Add segmentation and
paint name center of gravity queries.
- (01 Dec) Add Compress Front Face to the Surface: Geometry menu.
- (01 Dec) Add button to save the contents of the histogram dialog
to an image file.
- (06 Dec) Fix combining paint volumes so that the output volume
may be one of the input volumes.
- (06 Dec) Change separator characters in region of interest
reports to a semicolon instead of a tab.
- (07 Dec) Display translucent
uncertainty circles on
the volume slices if a "Node ID Deviation" column of the Surface Shape
file is enabled on the Display Control Dialog.
- (07 Dec) Increase initial width of Idenfity Dialog so that all of
toolbar is visable.
- (08 Dec) Add subject to header of SpecFile and allow it to be set
on the spec file dialog. If the species, subject, and hemisphere
are valid, new file names will default to
"species.subject.hem.file-type-name.date.num-nodes". "num-nodes"
is only present for node attribute files.
- (09 Dec) Add file extension to default file names.
- (14 Dec) Fix default peaks on histogram dialog.
- (14 Dec) Keep track of volume file type on Save Data
File Dialog and Import File Dialog.
- (14 Dec) Fixed problem with voxel crosshairs not jumping to
identified voxel in volume display.
- (14 Dec) When borders projected, make border projection file
"modified".
- (15 Dec) Update ".pro" files for FreeBSD O/S courtesy of Jason at
MCW.
- (15 Dec) Corrections for recently installed compress
front face.
- (15 Dec) Ignore nodes with names "GYRAL", "GYRUS", or "???" in
threshold probabilistic node coloring.
- (15 Dec) Display all paint volume names when a paint
volume voxel is selected.
- (16 Dec) Fix crash that occurred when a histogram dialog was
displayed without peaks.
- (16 Dec) Add labels and comments for sub-bricks in a
volume. When a multi-volume file is read into Caret, each
sub-brick
is stored in its own "volume-file" in memory. Labels and comments
can now be set for each of these using the "?" button on the view
current files dialog or on the display control dialog's
overlay/underlay - volume panel.
- (16 Dec) Add item to file menu to set current directory.
- (16 Dec) Add Text File Editor to File menu.
- (20 Dec) Add probabilistic atlas volumes.
- (20 Dec) Fix bug with handle finding crashing.
- (20 Dec) Add item to Surface:Geometry menu to scale a
sphere to the surface area of the fiducial surface.
- (21 Dec) Add Layers:Compute Average Separation Between Border
Point Pairs.
- (21 Dec) Fix reading of an unusual AFNI volume whose Z origin was
large and in Inferior-to-Superior orientation.
- (22 Dec) Corrections/changes to volume probabilistic atlas normal
coloring to make voxels darker if ??? (undefined) names are
contributing to the voxel.
- (22 Dec) Fixed bug with new output volume naming on the Volume
Mathematics Dialog.
- (22 Dec) Fixed bug that did not update Display Control Dialog
probabilistic atlas volume panel when a probabilistic atlas volume was
loaded after loading the spec file.
- (22 Dec) Fix prob atlas threshold to paint conversion.
- (22 Dec) Added Volume:Probabilistic Atlas:Convert Probabilistic
Atlas to Functional which stores in the functional voxel the number
of valid identifications for that voxel in all probabilistic atlas
channels and areas that are enabled.
- (23 Dec) Changed display of voxel data in the Identify Dialog.
All functional, paint, prob atlas, rgb, and segmentation data is
shown for the voxel.
- (23 Dec) Fixed Import Data File dialog, had forgotten
to add Prob Atlas Volume type.
- (23 Dec) Fixed writing of volume data when the volume
data originated as a byte with a scale factor. For now, Caret
writes float volumes (unless RGB).
- (27 Dec) Added palette coloring
for surface shape.
- (27 Dec) Added positive and
negative minimum values for metric
coloring. This allows greater control over palette colors to
non-thresholded metric values.
- (27 Dec) Use "*" to separate file name in preferences
files since a space is a valid file name character.
- (27 Dec) Add ability to set color and thickness for surface
outline displayed over a volume slice.
- (28 Dec) Add export to minc volume. When reading a minc
volume use directional cosines for orientation.
- (28 Dec) Add progress dialog to deformation.
- (28 Dec) Print out paint names for which there are no
area colors when assigning node colors.
- (28 Dec) Improved 3D border drawing.
- (29 Dec) When Display Control Dialog is launched, default to O/U
- Volume page if there are volumes but no surfaces loaded.
- (29 Dec) Change volume cropping
stuff to that a volume may also
be made larger (now "resize" instead of "crop").
- (29 Dec) Enable Surface and
Volume anytime an anatomical volume
is loaded. A fiducial surface is no longer requried.
- (29 Dec) Add display of segmentation volume cloud in Surface and
Volume.
- (30 Dec) Change point assignment within closed border
to assume points have Z = 0.0.
- (30 Dec) Add Padding of segmentation volumes.
- (03 Jan 2005) Corrected problem with coord and topo files
sometimes showing up as "(FILE NOT FOUND)" on the spec file dialog.
- (03 Jan 2005) When deforming a node attribute data file (metric,
paint, etc) make sure it has a sufficient number of nodes so that it
will work with the deformation map file.
- (03 Jan 2005) Add Remove Islands to Volume: Segmentation menu.
- (05 Jan 2005) Changed Surface:Topology:Disconnect Islands to
Remove Islands.
- (05 Jan 2005) Added Topology
Error Report to Surface:Topology
menu. This performs a number of topological check to verify a
surface is correct.
- (05 Jan 2005) Add volume ROI paint percentage report.
- (07 Jan 2005) Added Topology Error Report to Volume: Segmentation
Volume. This approximately counts handles, cavities, objects.
- (07 Jan 2005) Add generatation of cerebral hull volume
to Volume: Segmentation menu.
- (10 Jan 2005) Fix 30 Dec change so that only assume points have Z
= 0.0 for border inclusion check if the non-negative only flag is false.
- (14 Jan 2005) Fixed problems with SureFit segmentation algorithm
so that the segmentation now matches that produced by the soon to be
old SureFit program.
- (14 Jan 2005) Add surface shape depth, surface shape curvature,
and paint sulcal identification to the SureFit segmentation process.
- (14 Jan 2005) Change Edit Volume Attributes Dialog so that it no
longer requires that the volume whose attributes are being edited is in
the main window. Instead, it warns the user, allowing the
user to continue or cancel.
- (14 Jan 2005) Add item to File menu to Close the current
spec file (reset caret to its startup state).
- (14 Jan 2005) Fix import of minc byte volume files to that 0 to
255 range is restored instead of being scaled 0 to 1.
- (24 Jan 2005) Additional information added to Surface Topology
Report Dialog.
- (24 Jan 2005) Do not allow assignment of a topology file to a
surface if the topology file references node numbers greater than the
number of coordinates in the surface.
- (25 Jan 2005) Add read and write support for NIFTI volume
files. Caret can read a NIFTI file that it writes but no NIFTI
files are available for testing at this time.
- (25 Jan 2005) Fixed problem with upload of Volume File pairs
(header and data) data file not receiving the proper parent ID when a
spec file is uploaded.
- (25 Jan 2005) When uploading files to SuMS make sure all of the
files exist prior to starting the upload.
- (26 Jan 2005) Modify data files for future support of XML
reading and writing. Change SumsFileListFile, GenericXmlFile and
CocomacConnectivityFile for new implementation of XML file reading.
- (26 Jan 2005) Add keyboard commands for controling the view of
brain models loaded in Caret.
- (27 Jan 2005) Added ability to write a coordinate file in
XML format with the coordinate data base64 encoded. This is just
for experimentation purposes at this time.
- (27 Jan 2005) Correct generation of lat/long for nodes with X=0.
They were getting long = 0 but should have been +90 or -90.
- (28 Jan 2005) Modify keyboard commands so that they use the same
control/shift keys as the mouse.
- (28 Jan 2005) Started adding a "transformation axis" that
will be used to project objects not in surface space into the surface
space.
- (28 Jan 2005) Added a new
drawing mode "tiles-links-nodes"
designed for use with surface editing. It first draw the surface
as lighted tiles using the current coloring. It then draws the
links and nodes in blue.
- (31 Jan 2005) Add option for metric/shape/volume math replace NaN
with zero.
- (31 Jan 2005) Fix problem with volume attribute operations
when the volume is in the main window.
- (2 Feb 2005) Update Mac OSX, Linux, and Windows version of
Caret5 to use QT 3.3.4.
- (2 Feb 2005) Fix errors in flat multi-resolution morphing caused
by 24 Jan 2005 change that checked for topology file compatibility with
coord files.
- (2 Feb 2005) Add transformation matrices available to each
loaded VTK model file.
- (3 Feb 2005) Switch mouse mode between view and transformation
axes when the axes are clicked with the mouse.
- (3 Feb 2005) Modify rotation of transformation axes so that the
mouse and keyboard controls rotate and pan in screen space.
- (3 Feb 2005) With a surface or volume viewed, pressing the
"m, l, d, v, a, p, r " keys switches to the default view medial,
lateral,
dorsal, ventral, anterior, posterior, and reset.
- (4 Feb 2005) Now have
thresholding separate for each column in a
metric file. Thresholds are initially set while mapping
functional volumes. Also, an option has been added to show below
threshold
nodes in green.
- (7 Feb 2005) Corrections for spherical lat/long border generation.
- (8 Feb 2005) New "average" threshold column for metric and set
the average threshold during mapping of a functional volume.
- (8 Feb 2005) Allow application of a transformation matrix to
border, cell, foci, and vtk model files.
- (8 Feb 2005) Add writing of VTK model files.
- (9 Feb 2005) Change SuMS interface so that files are sorted by
most recent date.
- (9 Feb 2005) Modify transformation matrix dialog to get the
matrix from displayed surface or transformation axes and transfer
matrix to transformation axes view. Also load view for volume or
surface and volume. Apply matrix to surface and volume.
- (9 Feb 2005) Replace scale bar with axes that optionally show
tickmarks and orientation labels.
- (10 Feb 2005) Corrections for latitude and longitude +/-.
- (10 Feb 2005) Combine the Map
Functional Volume to Metric and the
Map Paint Volume to Paint File into a single item on the Attributes
Menu named Map Volume(s) to Surface(s).
- (11 Feb 2005) Add volume
montage display mode controlled on the
Display Control Dialog's Overlay/Underlay - Volume panel.
- (15 Feb 2005) Fix problem with an OpenGL error when selecting a
transformation axis with the mouse.
- (15 Feb 2005) Fixed appending of Transformation Matrix Files.
- (17 Feb 2005) Add ability to view a transformation matrix as a
set of coordinate axes.
- (21 Feb 2005) Add Show Deformation Variability to Surface:
Deformation menu.
- (21 Feb 2005) Added FLIRT and
MRITOTAL fmri mapping data files.
- (21 Feb 2005) During deformation, set the configuration_id to
flat or spherical for the resampled deformation borders.
- (23 Feb 2005) Add info to project cells/foci dialog, that in most
cases, the fiducial surface must be in an AC centered space.
- (25 Feb 2005) Add ability to read some files (cells, foci, and
vtk models) that are displayed in the space of a transformation matrix
axes.
- (3 Mar 2005) Correct origin for AFNI Talairach volume provided by
VolumeFile.
- (9 Mar 2005) Add initial implementation of automatic error
correction to segmentation process.
- (10 Mar 2005) Create some default matrices for AC to Native and
Native to AC transformations.
- (11 Mar 2005) Create a command line program "caret_volume" for
performing operations on volumes at the command line. Current
capabilities
include thresholding and segmentation.
- (14 Mar 2005) Remove spaces from surface type names in
BrainModelSurface which fixes a bug for file names added to the spec
file on MS Windows.
- (14 Mar 2005) Fix date in default file naming for windows which
was putting in the memory address instead of the date.
- (14 Mar 2005) Add new dialog for creating the name of a spec file
when the user chooses to create a spec file.
- (14 Mar 2005) Fix problem with Compressed Medial Wall surface
being upside down during flattening. I'm not sure what caused
this but
it may have been caused by some of the transformation changes made in
February.
- (14 Mar 2005) When a topology file is loaded, update topology
selection on the surface ROI dialog.
- (15 Mar 2005) On Flatten Hemisphere Dialog, try to automatically
determine if the fiducial surface is AC-centered.
- (15 Mar 2005) Add button to Volume Attributes Dialog to set a
volume's origin using the Main Window Crosshairs as the Anterior
Commissure location.
- (16 Mar 2005) Add a scroll
widget for contents of the Display
Control Dialog due to its panels becoming too large for some monitors.
- (16 Mar 2005) Add padding to partial hemisphere segmentation.
- (17 Mar 2005) Add a check in flat deformation to ensure that both
source and target have borders that begin with the name "LANDMARK",
"landmark", "morph.", or "MORPH.". The flat_fluid program only
uses borders with these extensions.
- (21 Mar 2005) When generating a surface from a segmentation,
remove any islands.
- (21 Mar 2005) Put lots of C-library functions such as sqrt or
atan in the std:: namespace which is required by the Borland C++
compiler for MS Windows.
- (22 Mar 2005) Correct problem with volume cropping crosshairs
sometimes incorrectly being shown.
- (25 Mar 2005) If the only
command line argument passed to Caret5
is a spec file, automatically load the Spec File into the Spec File
Dialog. This allows Microsoft Windows User's to double
click spec
files to start
Caret5.
- (25 Mar 2005) When writing a Volume File, set the file type
(AFNI, SPM, etc) based upon the header file's name's extension.
- (25 Mar 2005) Fixed crash that occurred when Cancel button was
pressed on Create Spec File Name Dialog.
- (25 Mar 2005) Make sure there is surface coloring after the
initial stage of flattening a full hemisphere.
- (25 Mar 2005) Fix bug that occaisionally erroneously reported
premature end of file when reading a Palette File.
- (25 Mar 2005) Change a couple of float spin boxes on the
Deformation - Flat Dialog to line edits due to a problem noticed only
on Linux.
- (25 Mar 2005) When reconstructing a volume to a surface, set the
surface's orientation to the volume' s orientation.
- (28 Mar 2005) Remove progress dialog when deformation exists due
to an exception such as a missing file.
- (28 Mar 2005) Hide volume to surface mapping dialog while
operation is executing.
- (28 Mar 2005) Pack items on various display control dialog pages
to take up less space.
- (28 Mar 2005) Identify Dialog: do not display voxel info when "V"
is unselected, remove "N" node option, change "All" to "All-N" for all
node information.
- (30 Mar 2005) Rearranged some items on the Display Control
Dialog's Overlay/Underlay pages for both surface and volume.
- (31 Mar 2005) Add a "Deselect All" to the Spec File Dialog to
deselect all files.
- (31 Mar 2005) Change volume drawing so that there is only one
threshold, not a min and max.
- (31 Mar 2005) Embed a histogram dialog into the SureFit
segmentation dialog to set the anatomy volume's gray and white matter
peaks.
- (31 Mar 2005) NOW VERSION 5.2.
- (1 Apr 2005) Allow volume specified in spec file to be minc
volumes.
- (1 Apr 2005) If Open Data File Dialog is used to open a border
file and there is no configuration_id in the border file, allow the
user to specify the type of border file.
- (4 April 2005) Add ability to delete the border projection file
on
the view current files dialog.
- (4 April 2005) If the user tries to open a coordinate or topology
file
of an unknown type, ask the user for the type of the file.
- (4 April 2005) When reconstructing a segmentation volume into a
surface,
a hole in the surface will result if any voxels in the edges slices are
on.
So, during reconstruction, pad the volume by one slice to prevent
this
problem.
- (4 April 2005) Fix problem with column widths for metric and
paint that occurred when the display control dialog was displayed prior
to loading a metric or paint file.
06 April 2005 - Release Caret 5.2
- (8 April 2005) Fixed independent surface coloring.
- (13 April 2005) Initial
implementation of scene which saves the state of overlays and
underlays, windows open, window contents, and window positions.
This data file is in XML format.
- (13 April 2005) Mac users can
now start Caret5 by double-clicking a spec file in the finder.
Prior to double-clicking any spec file for the first time, the user
must press the mouse once to select the and choose Get Info from
Finder's File Menu. Click the menu below "Open with:" and select
other and then find the Caret5 application.
- (13 April 2005) Speed up node coloring when a surface has
identical coloring as the first brain model.
- (13 April 2005) Remove SureFit Crossover Check and set primary
overlay to crossovers if any crossovers are found.
- (13 April 2005) When using SureFit Segmentation Dialog to set the
anatomy volume histogram, draw the thresholded regions in translucent
green.
- (13 April 2005) Do not require that voxel sizes be 1.0 in SureFit
Segmentation.
- (13 April 2005) Require voxel range in SureFit Segmentation to be
[0, 255].
- (14 April 2005) Add a multi-slice volume view that shows the
horizontal, parasaggital, and coronal views in one window. This
view is selected by selecting "All" from the volume slice control in
the main or viewing window toolbar.
- (14 April 2005) Change version to 5.201.
- (14 April 2005) Added an option on the spec file dialog to select
a transformation matrix. If a matrix is selected, the matrix will
be applied to raw and fiducial border, cell, coord, foci, and volume
files.
- (15 April 2005) Add identification to volume slice ALL view.
- (15 April 2005) Fix comment updater for XML files.
- (15 April 2005) When saving scenes, always save highlighted
nodes, properly use deformation field vectors, and always save surface
shape.
- (15 April 2005) Position Display Control and Identify Dialogs and
Viewing Windows just off the Main Window.
- (18 April 2005) Fixed setting of palette from a scene file.
- (18 April 2005) Fixed widths of some sub-widgets on D/C Dialog.
- (18 April 2005) Add Save As Image pushbutton to D/C Dialog.
- (18 April 2005) Changes made to read newer CoCoMac files.
On Open Data File Dialog, allow CoCoMac files to use ".xml" extension.
- (18 April 2005) Add copy sub-volume to segmentation volume
editing.
- (18 April 2005) Add volume label to Save Data File Dialog.
- (19 April 2005) Caret5 was
crashing on a Windows XP system while "initializing data" during Spec
File loading. OpenGL library vendor was listed as Intel.
Installing Microsoft's software OpenGL libraries into Caret5's "bin"
directory eliminated the problem.
- (20 April 2005) Add ability to generate create a segmentation by
just thresholding an anatomical volume.
- (20 April 2005) When generating a surface from a segmentation
volume allow the user to choose between generating a brain model
surface or a vtk model file.
- (20 April 2005) Add a segmentation voxel editing mode that allows
the user to select a piece of segmentation and discard all segmentation
voxels not connected to the selected voxel.
- (21 April 2005) Add option on Display Control Dialog's Surface
and Volume page to inhibit drawing of black voxels when volume slices
are drawn.
- (21 April 2005) Correct reading of VTK model files.
- (21 April 2005) Add option to set volume coordinates using Params
File's Whole Volume AC location.
- (21 April 2005) Add default transformation matrices if AC Whole
Volume parameters available.
- (21 April 2005) Add identification of VTK model files.
- (21 April 2005) Add scene saving for Surface and Volume
parameters.
- (22 April 2005) On MS Windows, sometimes received a "File is not
writable" message. Code to check for file being writable has been
disabled. May be a Samba issue
(http://lists.trolltech.com/qt-interest/2004-01/thread00623-0.html).
- (26 April 2005) Modify scene
implementation so that it keeps track of all loaded files. If
files needed for a scene are not in memory, Caret5 will automatically
load them so that the scene is correctly displayed.
- (26 April 2005) Add opacity for VTK model display.
- (26 April 2005) Transformation Matrix Editor. When a new
matrix is created, allow the user to choose the default values from an
identity matrix, the current matrix, the current volume slices'
stereotaxic coordinates, or the item at the center of the window when a
surface is displayed.
- (26 April 2005) Show axes letters (x, y, z) for transformation
axes in volume view.
- (27 April 2005) Modify saving of scene for transformation axes
display.
- (27 April 2005) Add Layers Menu items for converting borders,
cells, and foci to VTK models.
- (27 April 2005) Fix flickering hourglass during volume
segmentation voxel editing.
- (27 April 2005) Add scene replacement on Display Control Dialog's
Scene page.
- (27 April 2005) Changed copy spec file so that it always copies
the scene file. This is necessary since the scene file contains
paths that are typically relative to the spec file.
- (27 April 2005) When user is saving a scene, warn user if there
are any unsaved data files (except scene file).
- (27 April 2005) Add a scene filter button on the Spec File Dialog
toolbar.
- (28 April 2005) Various changes for scene processing.
- (28 April 2005) Fixes for one millimeter error in coordinates of
WU NIL ifh volumes.
- (28 April 2005) Show name of spec file on the View Current Files
Dialog.
- (28 April 2005) Add button on volume attributes to set the
spacing and origin for a volume using standard stereotaxic space
parameters. Only those spaces with matching dimensions are shown.
- (28 April 2005) Update projected files when surface scaled or
translated.
- (29 April 2005) Update non-projected files (borders, foci, cells)
when surface scaled or translated.
- (29 April 2005) Add a voxel scaling operation to the Volume
Attributes Dialog's Data page.
- (29 April 2005) Made some fixes for scene operations with
cocomac, prob atlas, and node IDs.
- (3 May 2005) Add many more operations to the command line program
"caret_ volume".
- (4 May 2005) When reset button in toolbar is pressed, it is
possible that the voxel with the (0, 0. 0) stereotaxic coordinate may
be outside the volume. In this case, get as close to this voxel
as possible.
- (4 May 2005) Fixed drawing of volume borders.
- (4 May 2005) Corrected label on Transformation Matrix Dialog for
applying a transformation matrix to a volume.
- (5 May 2005) Fix bug with volume border drawing.
- (5 May 2005) Fix bug with applying volume rotation.
- (5 May 2005) Initial
implementation of volume operation script
builder.
- (9 May 2005) Fix some scene bugs: small jumps in window
positions, deformation field never removed, surface outline color on
volume slice, and surface shape palette selection.
- (9 May 2005) Add image viewing
windows selectable from the Window menu.
- (10 May 2005) Fix display of scene files on Spec File Dialog when
all files shown.
- (10 May 2005) Incorporate image windows into scenes.
- (11 May 2005) Made changes to correctly read WU-NIL ifh volume
header files.
- (11 May 2005) Add a Print Main Window item to the file menu to
print an image of the main window. Note: printing does not seem
to work on Windows versions of Caret5.
- (11 May 2005) Add option to Volume Math Dialog to copy a volume.
- (12 May 2005) On Spec File Dialog, if only volume files are
shown, also show area colors files if there are any paint or prob atlas
volumes listed.
- (12 May 2005) When drawing borders on a volume, allow assignment
of paint volume voxel within the closed border.
- (12 May 2005) Add editing of paint volume voxels. Voxels
are editing similar to segmentation voxels in that the mouse pointer
functions as a paint brush.
- (13 May 2005) Transformation Matrix Editor - when new matrix
created, add option to set its values to the main windows view
transformation matrix.
- (13 May 2005) Scene fixes including failing to keep track of
files that are loaded via the toolbar's "spec" button. Remove
restrictions on names of scenes.
- (13 May 2005) Fixed bug that was failing to unregister closed
image windows that would cause Caret to crash at a later time.
- (13 May 2005) Eliminate some messages about data files modified
when saving or recreating a scene.
- (16 May 2005) Draw surface outline over volume slices using
triangles instead of links.
- (16 May 2005) In metric comment for mapping functional volumes to
surfaces, add the unit "mm" for neighbors in the comments.
- (16 May 2005) Limit width of channel and area pages for
probabilistic atlas on Display Control Dialog.
- (16 May 2005) Correct update of active fiducial surface on
Display Control Dialog's Surface Miscellaneous Page.
- (16 May 2005) Save active fiducial surface to the scene file.
- (16 May 2005) When mapping a volume to a multi-fiducial atlas,
list the surfaces in alphabetical order.
- (16 May 2005) When a coordinate file is saved, the topology file
used by the coordinate file is placed into the header of the coordinate
file. When loading the coordinate file and its cooresponding topo
file is not loaded, automatically load the needed topo file.
- (16 May 2005) Check for duplicate node attribute file column
names when creating/replacing or showing a scene.
- (17 May 2005) When mapping a volume to multiple surfaces, try to
determine the case name and include case name in the metric data column
name.
- (17 May 2005) While uploading files to SuMS, hide the SuMS
interface dialog.
- (17 May 2005) Fixed bug that caused the "map to caret" buttons on
the volume to surface mapper dialog to be incorrectly disabled.
- (17 May 2005) Do not let the Animate or Histogram buttons on the
Display Control's Metric page be the default button.
- (17 May 2005) If a spec file is loaded and only scene files were
selected, popup the Display Control Dialog and show its scene page.
- (18 May 2005) Add option to determine the minimum and maximum
columns when performing multi-fiducial mapping of functional volumes to
surfaces.
- (18 May 2005) When showing all 3 volume slices in a window, also
show the fiducial surface.
- (18 May 2005) When uploading a scene file to SuMS, strip the
paths off any of the files listed in the SpecFile section of the
SceneFile.
- (19 May 2005) Add opacity for volume overlays.
- (19 May 2005) Minor changes for items on map volume to surface
dialog.
- (19 May 2005) Add average for math operations on metric, shape,
and volume files.
- (20 May 2005) Add choice of color for identified node symbols on
the Display Control Dialog's Surface Miscellaneous page.
- (20 May 2005) Remove all model viewing windows when changing the
scene.
- (20 May 2005) Make entry of volume thresholds when mapping
functional volumes optional.
- (23 May 2005) Add an Image Editor to File Menu that allows
viewing and editing (annotating, cropping, and resizing) of images.
- (24 May 2005) Add item to Layers menu to copy the volume borders
to the fiducial borders.
- (24 May 2005) Add item to Volume Menu to create a new volume.
- (24 May 2005) Add image opening and saving to image editing
window.
- (24 May 2005) Enhance the text file editor.
- (25 May 2005) Fixed bug with replacing a scene. Now saves
all settings, not just those for selected data types.
- (25 May 2005) Fix crash caused by a color palette referencing a
non-existant color.
- (26 May 2005) Correct reading and writing of AFNI volume origins.
- (26 May 2005) Add printing to image editor window.
- (26 May 2005) Add printing to the text file editor.
- (27 May 2005) Add some additional operations: find limits,
intersect volume with surface, make plane, and pad volume to the
caret_volume command line program. Updated script builder for
these new commands.
- (31 May 2005) When applying a transform to a volume use nearest
neighbor interpolation for paint, prob atlas, segmenation, and rgb
volumes and cubic interpolation for anatomical and functional volumes.
- (31 May 2005) On Transformation Matrix Editor, correct loading of
main window volume view transform.
- (31 May 2005) Fix possible problem with current directory being
altered when mapping a volume to a surface.
- (31 May 2005) Allow specification of voxel data type when writing
a volume file. Save Data File dialog only shows voxel data types
that are valid for the type of volume file selected.
- (1 June 2005) Corrected problem with mapping to multi-fiducial
but only outputting the average.
- (1 June 2005) When saving a volume file, warn user if the voxel
values of the volume are outside the valid values for the selected data
type.
- (1 June 2005) Change display of images so that the center of the
image is placed in the center of the main window.
- (1 June 2005) Set the Z value of an image so that it is "far
behind" the model in the main window.
- (1 June 2005) Fix problem with main window resize handle not
being on the right side of the status bar.
- (2 June 2005) Add some more information to error message during
deformation of a border projection file.
- (2 June 2005) Add the program "caret_edit" for editing text
files. This is just a stand alone version of the text file editor
available on the File Menu. This simple text editor handles all
of the different platform dependent line feeds.
- (3 June 2005) Fixed bug with brain model viewing windows only
showing up some of time when a scene was selected. The GUI system
need to time to process its events so that it could close the windows
when a scene was selected, prior to reopening the windows.
- (6 Jun 2005) fMRI Mapping: average fiducial coord file now added
to atlas spec files. Selection of average, deviation, etc. is now
made each time a mapping atlas is selected.
- (6 Jun 2005) When saving a gzipped volume, make sure ".gz"
extension is on the data file's name in the spec file.
- (6 June 2005) Add "Load Scene(s)" push button to Spec File
Dialog. This will load all scene files and nothing else.
- (7 June 2005) When loading node attribute file (metric, paint,
etc) from Open Data File Dialog or Toolbar Spec button, if Erase All
Columns is selected, switch the comment option to Replace.
- (7 June 2005) Require at least an overlay or underlay volume for
drawing borders on volumes.
- (7 June 2005) When the viewed image in an image viewing window is
changed by the user, preserve the view scaling.
- (7 June 2005) Fixed deletion of surface shape file on view
current files dialog.
- (7 June 2005) On both Open and Save Data File Dialogs, corrected
saving of previous directories (was one level too high) and update
viewed files using selected filter when a previous directory is
selected.
- (7 June 2005) Add separate control for display of palette color
bar on volume display.
- (7 June 2005) Change version to 5.3.
- (7 June 2005) If there is a selected deformation map file, make
it the default deformation map on the Apply Deformation Map Dialog.
- (7 June 2005) When showing a scene, avoid closing any model
viewing windows that are needed by the new scene.
- (7 June 2005) Fix crash that occurred when the Display Control
Dialog was popped up for the first time after opening and closing a
model viewing window.
- (8 June 2005) Add more mathematical operations for metric, shape,
and volume. New operations set a range of values (inclusive or
exclusive) to zero.
- (8 June 2005) Add slice thickness when drawing volume borders.
- (8 June 2005) Default rotation for surfaes is now XY.
- (8 June 2005) Fix so opacity for VTK models allows transformation
axes to be seen.
- (9 June 2005) Hide SuMS Database Dialog while files are
downloading.
- (9 June 2005) Add Identify Dialog to scenes.
- (10 June 2005) Avoid scrolling list of scenes in Display Control
Dialog when a scene is selected for viewing.
- (13 June 2005) In the caret_volume program, disregard the debug
on setting in the user's preferences file. When caret_volume is
run from Caret's script builder and output from caret_volume is 8173
characters, caret_volume gets stuck writing I/O. caret_volume
still works fine from the command line.
- (13 June 2005) Fix size of model combo box on model viewing
windows.
- (13 June 2005) Make Display Control: Shape: Settings page wider
so full name of palette may be seen.
- (14 June 2005) Use full path to caret_volume program in volume
script builder. Warn if the environment variable CARET_DEBUG is
on since excessive output causes programs executed with QProcess to
hang.
- (14 June 2005) Fix command line switch for make sphere operation
in caret_volume program.
- (17 June 2005) Add scene insertion.
- (17 June 2005) Print more information if Caret runs out of memory
including an option to exit Caret.
- (17 June 2005) Add option on Display Control Scene page to cycle
through scenes and verify that they are valid.
- (17 June 2005) Add ability to send scenes from one Caret
application to another.
- (20 June 2005) Various fixes for caret_volume command line
program.
- (20 June 2005) Fix Volume to Surface Mapper for Mapping
Individual to Spec File.
20 June 2005 - Release Caret 5.3