

Caret5
Tutorial
Segmentation,
Flattening, and Registration
John
Harwell, Donna
Hanlon,
Heather
A. Drury,
and David C. Van Essen
Version
5.5
September
2006
Copyright
1995-2006
Washington University
Washington
University School of Medicine
Department
of
Anatomy and Neurobiology
Saint
Louis,
Missouri USA 63110
http://brainmap.wustl.edu
Table of
Contents..................................................................................................................
2
Table
Of
Figures...................................................................................................................
3
Copyright
2006 Washington
University..................................................................................
5
About
This
Document............................................................................................................
6
Conventions
in this
Document................................................................................................
6
Bug
Reporting or Questions About Caret5
Software.............................................................. 6
Downloading
and Installing
Caret5.........................................................................................
6
Data
Set for Use With This
Tutorial.......................................................................................
6
Prerequisites..........................................................................................................................
7
Volume
File Types Supported by
Caret5...............................................................................
7
Set the
Current (Working)
Directory......................................................................................
7
Read
the Anatomical
Volume.................................................................................................
8
Anatomical
Volume
Requirements..........................................................................................
9
Set the
Volume’s
Orientation...............................................................................................
10
Set the
Volume’s Stereotaxic
Coordinates...........................................................................
11
Setting
the Voxel Range to 0 to
255.....................................................................................
14
Saving
the Anatomical
Volume.............................................................................................
14
Cropping
the Anatomical Volume to a Single
Hemisphere..................................................... 15
Segmenting
an Anatomical
Volume......................................................................................
18
Manual
Error
Correction.....................................................................................................
26
Error
Correction
Example................................................................................................
30
Save
Corrected Segmentation
Volume.............................................................................
34
Generating
Final Surface and Surfaces For
Flattening........................................................... 34
Surface
Flattening................................................................................................................
36
Correct
Template Medial Wall Boundary and Calcarine Cut
Borders............................... 37
Multi-Resolution
Morphing (Surface Distortion
Reduction)............................................... 41
Aligning
the Surfaces to Standard
Orientation...................................................................
41
Saving
the Aligned Surface
Files......................................................................................
43
Spherical
Registration..........................................................................................................
46
Command
Line
Segmentation..............................................................................................
52
Figure 1 - Choose Current Directory
Dialog...........................................................................
8
Figure 2
- Import Data File
Dialog.........................................................................................
9
Figure 3
- Volume with Intensity
Problems...........................................................................
10
Figure 4
- Volume Attributes Editor
Dialog..........................................................................
11
Figure 5
- Crosshairs Near
Ventricles..................................................................................
12
Figure 6
- Crosshairs Over AC in Parasaggital
View............................................................ 13
Figure 7
- Crosshairs Over AC in Horizontal
View............................................................... 13
Figure 8
- Save Data File Dialog for Saving Anatomical
Volume........................................... 15
Figure 9
- Cropping Right Hemisphere Horizontal
View....................................................... 16
Figure
10 - Cropping Right Hemisphere Parasagittal
View.................................................... 16
Figure
12 - Cropped Right
Hemisphere...............................................................................
17
Figure
13 - Save Data File Dialog - Cropped Right
Hemisphere........................................... 18
Figure
14 - SureFit Operations Set Directory
Page.............................................................. 19
Figure
15 - SureFit Operations Subject Information
Page..................................................... 20
Figure
16 - SureFit Operations Spec File
Page....................................................................
21
Figure
17 - SureFit Operations Volume Selection
Page........................................................ 22
Figure
18 - Segmentation Operation Volume Attributes
Page............................................... 23
Figure
19 - SureFit Operations Set Gray and White Matter Peaks
Page............................... 24
Figure
20 - Segmentation Operations
Page..........................................................................
25
Figure
21 - SureFit Operations Segmentation Complete
Page............................................... 26
Figure
22 -
Segmentation.....................................................................................................
27
Figure
23 - Segmentation Near
Eye.....................................................................................
27
Figure
24 - Segmentation Near Eye
Corrected.....................................................................
28
Figure
25 - Midbrain Before
Correction...............................................................................
29
Figure
26 - Midbrain After
Cleanup.....................................................................................
29
Figure
27 - Segmentation Volume Handle Finder
Dialog....................................................... 30
Figure
28 - Handle Voxels Highlighted In
Purple..................................................................
31
Figure
29 - Handle Voxels Without
Highlighting...................................................................
31
Figure
30 - Anatomical Volume in Handle
Region................................................................ 31
Figure
31 - Voxels That Need to Be Remove to Fix
Handle................................................. 32
Figure
32 - Handle in
Surface..............................................................................................
32
Figure
33 - Segmentation Volume Editor
Dialog...................................................................
33
Figure
34 - SureFit Operations Volume Selection (Segmentation
Volume)............................ 35
Figure
35 - Segmentation Operations Page (Final
Surfaces).................................................. 36
Figure
36 - Flatten Full Hemisphere
Dialog..........................................................................
37
Figure
37 - Template Cuts on Compressed Medial Wall
Surface.......................................... 38
Figure
38 - Identifying Medial Wall and Calcarine on Inflated Surface in
Medial View........... 39
Figure
39 - Identified Medial Wall and Calcarine Cut on Compressed Medial Wall
Surface.. 39
Figure
40 - Corrected Medial Wall and Calcarine Cut on Compressed Medial Wall
Surface. 40
Figure
41 - Initial Flat
Surface..............................................................................................
41
Figure
42 - Unaligned Flat
Surface.......................................................................................
42
Figure
43 - Aligned Flat
Surface..........................................................................................
43
Figure
44 - Save Aligned Flat Coordinate
File......................................................................
44
Figure
44 - Node Identified Along Superior Temporal
Gyrus................................................ 47
Figure
46 - Central Sulcus, Superior Temporal Gyrus, and Sylvian Fissure
Landmarks.......... 48
Figure
46 - Landmarks on
Flat............................................................................................
49
Figure
47 - Landmarks on
Sphere.......................................................................................
49
Permission
to use, copy, modify, and distribute this document solely for
non-commercial applications
is hereby granted by Washington University free of charge, provided
that the
copyright notice "Copyright 2006 Washington University" appears on
all copies of the software and that this permission notice appears in
all
supporting documentation. The name of Washington University or of any
of its
employees may not be used in advertising or publicity pertaining to the
software without obtaining prior written permission from Washington
University.
Washington
University makes no representation about the suitability of this
software for
any purpose. It is provided "as is" without any express or implied
warranty.
This
document is designed to serve as a tutorial on how to segment and
flatten
surfaces using Caret5.
- All tutorial steps are identified by bullets.
- Actions the user should take are in italics.
- User-interface components are in BOLD.
Please
use either the Caret users’ mailing list (http://brainmap.wustl.edu/resources/caretnew.html#Help)
or send an email to caret@brainmap.wustl.edu.
Suggestions are also welcome.
Please
see the document Caret
5.5 Tutorial – Introduction, Installation, and Visualization.
The
data set for use with this tutorial is available in “zip” format from
our SuMS
database. Follow the link http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6588227.
On the SuMS web page, there is column named name
containing the file name: caret_5.5_segment_flatten_register_tutorial.zip.
To the left of this name in the action
column
is a control. Select
this
control, which will popup a menu, and select
download to
automatically start
downloading the archive (set of files).
After
downloading the data set, the archive needs to be uncompressed.
Linux and
Macintosh users should run
the
command unzip
caret_5.5_segment_flatten_register_tutorial.zip.
Windows XP users
should place the mouse
over the
downloaded file and press
the
right mouse button. From the popup menu, choose Extract All and follow
the prompts. Windows XP users may also extract the file from the
command line
window by running caret_unzip
caret_5.5_segment_flatten_register_tutorial.zip provided the
caret/bin directory is in the user’s PATH environment variable.
This
document assumes the reader has some familiarity with Caret5 such as
the
ability to view surfaces and volumes, use the Display Control Dialog,
and
manipulate borders. Please see one of the other tutorials if you
are not
familiar with viewing data in Caret5.
Volume
files of type AFNI, NIFTI, SPM, and Washington University’s “.ifh”
format are
read using the Open Data File
item
on the File Menu.
These volumes
have sufficient metadata that specifies the orientation and stereotaxic
coordinates. If a volume of one of these types is used, some of
the steps in
this tutorial will not be necessary.
Volume
files of type Analyze, MINC, and VTK are read using the Import File menu item on the File Menu. These file
types rarely have
sufficient metadata and it will usually be necessary to set some of the
volume’s attributes using Caret5 prior to segmenting the volume.
While most
MINC volumes contain the required metadata, those MINC volumes written
by
SureFit (used for segmentation and distributed by our lab prior to this
release
of Caret5), do not contain the required metadata.
In
this tutorial, an Analyze format volume file will be used that will
require the
setting of attributes in Caret5.
Prior
to starting Caret5, place the anatomical volume (tutorial data set
files) into
a directory containing no other files. Start Caret5 using the
appropriate
method for your operating system. If you do not start Caret5 from
a terminal
window with the current directory set to the directory containing the
anatomical volume, perform the following steps to set the current
directory:
- Select Set Current Directory from the File Menu to launch the Choose Directory Dialog.
- Using the Choose
Directory Dialog, navigate
to the directory containing the anatomical volume as shown in Figure 1
and press the OK button.

Figure 1
- Choose Current Directory Dialog
Import
the Analyze Volume by performing the following steps:
- Select Import File from the File Menu.
- In the Import
Data File Dialog, verify that the File type control is set to Analyze Volume File (*.hdr) and
that the Volume Type in
the Import Selections
section is set to Anatomy.
- In the Import
Data File Dialog, highlight
the file named Human.case9.LR.711-2C.hdr as shown in Figure 2 and press the Open button to load the file.

Figure 2
- Import Data File Dialog
A
volume must meet several requirements to be segmented in Caret5.
These
requirements are:
1)
The
volume must be standard
T1-weighted
MRI scans taken in vivo, in which white matter is bright, gray matter
is darker,
and CSF is even darker.
2)
The intensities should be consistent
throughout the volume. For instance, in Figure 3, the frontal lobes
are much brighter than the remainder of the brain. This volume
would not be segmented correctly.
3)
The
volume must be in an LPI orientation. That is, the negative X is
left,
negative Y is posterior, and negative Z is inferior.
4)
The
voxels must be 1mm cubic voxels (0.5mm for monkeys).
5)
The
volume’s stereotaxic coordinates must be set so that the coordinate (0,
0, 0)
is at the anterior commissure.
6)
The
volume must contain only a single hemisphere or part of a single
hemisphere.
7)
The
voxels must be in the range 0 to 255.

Figure 3
- Volume with Intensity Problems
We
know that the anatomical volume used in this tutorial is already in an
LPI
orientation but this information was not in the header file. Set
the volume’s
orientation by following these steps:
- Select Edit Volume Attributes from the Volume Menu to display the Volume Attributes Editor Dialog.
- In the Volume
Attributes section, select
the Orientation Tab by clicking it with the
mouse. The current orientation is set to X-Unknown, Y-Unknown,
and Z-Unknown.
- Press
the mouse over the X-Unknown
item and a menu will pop up listing the available choices. Change
the X-Unknown to X-Left to Right. Perform the same operation on
the Y-Unknown and Z-Unknown items so that they read Y-Posterior to
Anterior and Z-Inferior to Superior respectively as shown in Figure 4.
- Press
the Apply button to
apply these changes to the volume.

Figure 4
- Volume Attributes Editor Dialog
If
you use a volume type that has sufficient metadata that describes the
volume’s
orientation (such as an AFNI volume) Caret5 will automatically convert
the
volume to an LPI orientation. Otherwise, the Flip About X Screen
Axis, Flip
About Y Screen Axis, and Rotate Clockwise buttons in the Orientation
section of
the Volume Attributes Editor can be used to bring the volume into an
LPI
orientation.
Now
that the volume’s orientation has been set, the volume’s stereotaxic
coordinates need to be established. The voxel sizes are already
set to 1.0 mm
for each dimension. The origin values are the coordinates of the
voxel that is
the most left, posterior, inferior voxel. To set the origin, we
will find the
anterior commissure and inform Caret5 of its location. Caret5
will then use
the voxel sizes along with the anterior commissure position to
determine the
origin. Locate the Anterior Commissure so that it is under the
crosshairs in
the Main Window by performing the following steps:
- In the Main
Window hold down
the shift key, hold down
the left mouse button, and drag
the volume to that the entire volume slice is visible.
- Click
the mouse near the bottom of the anterior set of ventricles as shown in
Figure 5.
- Switch
to a parasagittal view by pressing
the mouse over the Volume Axis
Viewing Control in the toolbar (currently labeled H(XY)) and selecting P(YZ).
- Click
the mouse over the anterior commissure as shown in Figure 6.
- Switch
to a coronal view by changing
the Volume Axis Viewing Control
to C(XZ) to view the
crosshairs relation to the anterior commissure.
- Switch
back to a horizontal view. The selected slices should now read
88, 122, 73. If they do not, adjust them using the arrows in the Toolbar as shown in Figure 7.

Figure 5
- Crosshairs Near Ventricles

Figure 6
- Crosshairs Over AC in Parasaggital View

Figure 7
- Crosshairs Over AC in Horizontal View
Now
that the crosshairs are over the anterior commissure, the volume’s
stereotaxic
coordinates are established by performing the following steps:
- On the Volume
Attributes Editor Dialog, press the Coordinates Tab.
- Press
the Use Main Window Crosshairs as AC Location to
Determine Origin push button. After doing so, you will
see the origin values set to –88.0, -122.0, and –73.0.
- Press
the Apply button so
that the volume’s origin is updated.
- Press
the R (Reset) button on
the Main Window’s Toolbar
to set the view of the volume to the default view with the (0.0, 0.0,
0.0) stereotaxic coordinate at the center of the window.
- On the Volume
Attributes Editor, press
the Data Tab.
- Press
the Rescale Voxel Values
button.
- Change
the Output Range values
to 0 and 255 (or press the Set
button in the Output Range
row and selection the top item, Byte
– Unsigned.
- Press
the Close button on the
Volume Attributes Editor Dialog.
With
the volume’s attributes properly set, the volume should be saved by
following
these steps:
- Select Save Data File from the File Menu to display the Save Data File Dialog.
- Set the
File Type to Volume File –
NIFTI (*.nii *.nii.gz).
- In the Comment
section add a comment stating that the volume is now an AC centered
coordinate system volume.
- Leave the Write
Data File As set to Other.
- Verify
that the Volume Type is
set to Anatomy.
- Verify
that the Volume File is
set to Human.case9.LR.711-2C.hdr (the Analyze volume that was imported).
- Change
the File name to
Human.case9.LR.711-2B_AC_ORIGIN+orig.nii so that the Save Data File Dialog appears as
shown in Figure 8.
- Press
the Save button on the Save Data File Dialog to save
the volume file.
- When asked “Would you like to create a Spec File ?”,
click the Yes push button.
- In the Create
Spec File Dialog, set the Species to Human by selecting the Species push button and selecting human.
- Set the
Subject to case9.
- Set the
Hemisphere to Right (Note: even though we are
saving a full volume, in this tutorial we are going to segment the
right hemisphere).
- Select
the Space push button
and set the space to 711-2B-111 (which is the
stereotaxic space of the anatomy volume). This value is just for
informational purposes.
- Select
the Category push
button and set the
category to INDIVIDUAL.
- Press
the OK button on the Create Spec File Dialog.
As new files are created in Caret5, the information from the Create Spec File Dialog will be
used for default file names.
- In the Spec
File Name Dialog, the name of the spec file that will be
created (Human.case9.R.spec) using the information on the Create Spec File Dialog is
shown. Accept this name by pressing
the OK button.

Figure 8
- Save Data File Dialog for Saving Anatomical Volume
Caret5’s
segmentation algorithm requires that the input volume contain only a
single
hemisphere. In the next steps, the anatomical volume will be
cropped so that
it contains just the right hemisphere.
- Select Resize Underlay Volume from the Volume Menu.
- Press
the Reset button on the
Resize Volume if the
cropping boundary lines are not displayed on the volume in the Main Window.
- Press
the Up Arrow for the X Min parameter so that it is
set to 85 (or just enter 85 in the box).
- Press
the Down Arrow for the X Max parameter so that it is
set to 163.
- Press
the Up Arrow for the Y Min parameter so that it is
set to 15.
- Press
the Down Arrow for the Y Max parameter so that it is
set to 197 so that the volume cropping boundary lines appear as shown
in Figure 9.
- Change
to a Parasagittal view of the volume so that the Z cropping parameters
can be set by using the Volume
View Axis Control in
the Main Window Toolbar.
- Press
the Up Arrow for the Z Min parameter so that it is
set to 30.
- Press
the Down Arrow for the Z Max parameter so that it is
set to 158 so that the volume cropping boundary lines appear as shown
in Figure 10. Use a coronal view to assist in verifying that the
inferior part of the temporal lobe does not get cut off.
- Press
the OK push button on
the Resize Volume Dialog
to crop the anatomical volume.
- Press
the R button in the Main Window Toolbar to center
the view of the cropped right hemisphere. Note that the volume
crosshairs center on the Anterior Commissure.
- The cropped volume in a horizontal view
should appear as shown in Figure 12.

Figure 9
- Cropping Right Hemisphere Horizontal View

Figure 10
- Cropping Right Hemisphere Parasagittal View

Figure 12
- Cropped Right Hemisphere
The
cropped right hemisphere should be saved by performing the following
steps:
- Select Save Data File from the File Menu.
- Change
the File name to
Human.case9.R.RIGHT_HEM+orig.nii.
- Update
the comment to indicate
that it is a cropped right hemisphere so that the Save Data File Dialog appears as
shown in Figure 13.
- Press
the Save push button to
save the file.

Figure 13
- Save Data File Dialog - Cropped Right Hemisphere
Now
that you have a single hemisphere that is AC-centered, in LPI
orientation, with
1.0 mm cubic voxels, it is now time to start the segmentation process.
- Select SureFit Operations (Segmentation)
from the Volume Menu.
- The first page of the Surefit Segmentation
Operation Dialog is Change/Verify Current Directory page. The
directory already be set to the directory containing the volume files
as shown in .

Figure 14 - SureFit Operations
Set Directory Page
- The second page of the SureFit Segmentation Operations Dialog
is the Subject Information Page
as shown in Figure 15. This information is what was entered on
the Create Spec File Dialog.
Press the Next push button.

Figure 15
- SureFit Operations Subject Information Page
- The Spec
File Selection Page shows the Spec File that will be updated
as new data files are created during the segmentation process as shown
in Figure 16. If you had not created a spec file, the name for
the new spec file would be entered on this page. Press the Next push button to continue.

Figure 16
- SureFit Operations Spec File Page
- The Volume
Selection Page allows selection of the volume that will be
processed by the SureFit segmentation algorithm as shown in Figure
17. Press the Next push button to continue.

Figure 17
- SureFit Operations Volume Selection Page
- The Volume
Attributes Page describes requirements for the volume that
is to be processed by the SureFit segmentation algorithm as shown in
Figure 18. These requirements were met during previous steps of
this tutorial. Press
the Next push button to
continue.

Figure 18
- Segmentation Operation Volume Attributes Page
The Set
Gray and White Matter Peaks page is
used to provide information about the distribution of gray and white
matter in
the volume. On the left side of page is a histogram showing the
distribution
of voxels in the anatomical volume. On the right side of the page
are controls
for adjusting the gray and white matter peaks. Selecting the
round or diamond
shaped button to the left of Gray
Peak
Control or the White
Peak Control
colors all voxels exceeding that peak in green. Caret5 will
attempt to
identify the gray and white peaks but they normally will need some
adjustment.
For
additional information on drawing peaks visit the web page
http://brainvis.wustl.edu/help/peak_tweaking/index.html.
- Use the
Y-Max slider to
control the display of the histogram so that the peaks are easily
visible.
- Press
the arrows in the Gray Peak Control
so that the gray peak is set to about 57 (to the left of the actual
gray peak).
- Press
the arrows in the White Peak
Control so that the white peak is set to about 106 (just to
the left of the white peak)
- The Set
Gray and White Matter Peaks Page should appear as in Figure
19. Press the Next push button.

Figure 19
- SureFit Operations Set Gray and White Matter Peaks Page
- The Segmentation
Operations Page allows the user to choose the operations
that are to be carried out during the segmentation process. While
the SureFit algorithm attempts to identify and correct all topological
defects (handles), there are usually a few handles that the algorithm
is unable to correct. So, to save a little time, deselect the Generate Very Inflated Surface, Generate Ellipsoid Surface (used
for Flattening) and Create
Curvature, Depth, and Paint Attributes check boxes so that
the Segmentation Operations Page
appears as in Figure 20. Press
the Next push button.

Figure 20
- Segmentation Operations Page
- An Information
Dialog will appear informing you that any previously
generated surface files will be removed from the spec file and deleted
due to the fact they will be incompatible with the newly generated
surfaces produced by the segmentation process. Press the OK button and the segmentation
process will begin. This may take up to several hours depending
upon the speed of your computer. A progress dialog will be
displayed during the segmentation process indicating the step that is
being performed. The Automatic Error Correction step will take
the longest amount of time.
- At the conclusion of the SureFit Algorithm
the Segmentation Complete Page
will appear as shown in Figure 21. It will list the execution
time and, if a surface was generated, the number of topological defects
(handles) still remaining in the surface. Press the Close push button on the SureFit Segmentation Operations Dialog.

Figure 21
- SureFit Operations Segmentation Complete Page
In
most cases, there will be handles remaining after the initial
segmentation. In
addition, the SureFit algorithm may classify non-cortical material near
the eye
or in the midbrain as cortex. Arteries and blood vessels may also
get
segmented and are usually very bright in the anatomical volume.
As a result,
manual error correction must be performed. At times, this may be
an iterative
process in which multiple cycles of manual correction of the
segmentation
volume and surface generation are performed.
- Use the
Model Selection Control
to display VOLUME in
the Main Window.
- Press
the D/C button in the Main Window Toolbar to show the Display Control Dialog.
- Set the
Display Control Dialog’s Page
Selection so that the Overlay/Underlay
Volume page is shown.
- Set the
Underlay to Anatomy. Set the Primary Overlay to the newest
segmentation volume, most likely one with “Error_Corrected” in its name.
- Select Viewing Window 2 from the Window Menu.
- In Viewing
Window 2, display the FIDUCIAL
surface.
- Press M
in the Viewing Window 2’s Toolbar
to place the surface in a medial view. Look for non-cortical
material that may appear as shown in FIGURE??? and is shown by a green
symbol. Click on
the non-cortical material that is part of the fiducial surface and you
will see the volume slice and crosshairs
in the Main Window
relocate to the non-cortical material.
- The problems near the eye are found in
horizontal slice 14.

Figure 22 - Segmentation

Figure 23 - Segmentation Near
Eye

Figure 24 - Segmentation Near
Eye Corrected
- Switch
to a coronal view. Check for erroneous segmentation in midbrain
structures as in Figure 25. This part of the segmentation will
need to be removed.
- To edit segmentation voxels select Edit
Voxels from the Volume Menu’s Segmentation submenu.
- On the Segmentation Volume Editor, set the
Editing Mode to Turn Voxels Off.
- Set the Brush Size to 3x3 (or larger).
Press the Apply push button.
- Place the mouse over the midbrain structure
and hold down the left mouse button. The mouse will act as an
eraser. Continue moving the mouse around, with the left mouse
button held down, until all of the segmentation voxels that overlay the
midbrain structures have been removed. Use the middle slice
control in the toolbar to correct other slices that contain
segmentation voxels over the midbrain structures. Check slices
ranging from about 90 to 140.
In
some cases, it may not be necessary to remove all of voxels on the
midbrain
structures. Instead, just make sure that the voxels overlaying
the midbrain
structures no longer connect to the voxels overlaying the white and
gray
matter. Once you believe the segmentation voxels overlaying the
two structures
are no longer connected, select Remove Islands form the Volume Menu’s
Segmentation submenu. You might want to save the segmentation
volume prior to
using this option.

Figure 25
- Midbrain Before Correction

Figure 26 - Midbrain After
Cleanup
Now
that the voxels overlaying the midbrain structure have been removed it
is time
to look for handles (topological defects).
- Select Find Handles from the Segmentation sub-menu on the Volume Menu.
- In the Volume
Handle Finder Dialog, check
the box next to Y Axis (Coronal)
in the Search section.
- Press
the Search For Handles
push button in the Search section of the dialog. This will
require a few minutes to search the volume for handles. When
complete, the Volume Handle Finder
Dialog will appear similar to that in Figure 27 with
possibly different handles listed. Voxels that make up the “hole” of
the handle are colored in purple by creating an RGB Volume and
displaying it as the Secondary Overlay. For each handle found,
the dialog will list the slice indices of one voxel in the handle, the
number of slices along the search axis that the handle is within, and
the total number of “hole” voxels in the handle.

Figure 27
- Segmentation Volume Handle Finder Dialog
- Select Window 2 from the Window Menu.
- Use the
Model Selection Control
in the Viewing Window 2
to show the INFLATED
surface. Notice that surface nodes around handles are colored in
purple. It may be necessary to switch to a medial or ventral view.
- In the Handles
section of the Volume Handle
Finder Dialog, click
one of the listed handles with the mouse. The volume slices
should jump to the handle with the “inside” of the handle shown in
purple. Sometimes it is necessary to adjust the viewed slice by
one slice.
When
correcting errors in the volume it is sometimes helpful to turn off the
segmentation and the RGB coloring that shows the handles to view the
underlying
segmentation to help determine the type of correction necessary.
This
example is not from this tutorial’s segmentation. Here is an
instance where
the segmentation has jumped across the banks of a sulcus in the
occipital
lobe. Figure 28 shows the segmentation with the handle in purple,
Figure 29 shows the segmentation, Figure 30 shows just the anatomical
volume, Figure 31 shows the segmentation with the voxels that
should be removed in a black encircled region, and Figure 32 shows the
handle on the inflated surface.

Figure 28
- Handle Voxels Highlighted In Purple

Figure 29
- Handle Voxels Without Highlighting

Figure 30
- Anatomical Volume in Handle Region

Figure 31
- Voxels That Need to Be Remove to Fix Handle

Figure 32
- Handle in Surface
The
following steps are taken to correct this handle.
- Set the
Primary Overlay to
the Segmentation Volume.
- Set the
Secondary Overlay to
No Coloring (Removes
purple coloring of voxels inside the handle).
- Set the
Underlay to Anatomy.
- Select Edit Voxels from the Segmentation sub-menu on the Volume Menu.
- On the Segmentation
Volume Editor Dialog, set
the Editing Mode to Turn Voxels Off (In this mode,
the mouse pointer functions like an eraser removing segmentation voxels.
- Set the
Brush Size to 3x3. This means that when
the mouse is clicked or dragged (moved with the left mouse button held
down) over a voxel, the voxel and its eight surrounding neighbors in
the slice will be affected by the segmentation editing operation.
Leave the Brush Thickness set at Current Slice Only so that only
segmentation voxels in the current slice will be modified. The Segmentation Volume Editor
should appear as shown in Figure 33.
- Press
the Apply push button
on the Segmentation Volume Editor
Dialog.
- Place
the mouse over a segmentation voxel that is fusing the banks of the
sulcus together. Hold down
the left mouse button and drag
the mouse over the voxels that are causing the problem. When the
offending voxels are removed, release
the mouse button.

Figure 33
- Segmentation Volume Editor Dialog
Correcting
handles involves adding voxels to the segmentation or removing voxels
from the
segmentation. When voxels need to be removed from the
segmentation, set the Editing Mode
of the Segmentation Volume Editor
to Turn Voxels Off.
When voxels need to be
added, set the editing mode of the Segmentation
Volume Editor to Turn
Voxels On.
The mouse will function as an eraser or a paint brush. After
making any
changes to the Segmentation Volume
Editor
Dialog, press the dialog’s Apply
push button. In the Main Window
with the segmentation volume displayed, just move the mouse with the
left mouse
button held down to change the status of segmentation voxels. If
there is a
hole in a slice that needs to be filled, set the Editing Mode to Flood Fill 2D.
Clicking the mouse on a voxel
that is not part of the segmentation will fill all connected voxels
that are
not part of the segmentation. If at any time a mistake is made
while editing
the surface, pressing the Undo
push button will restore the values of voxels that were just
changed. It may
be necessary to press the Undo
push button several times to back out changes.
When
using the Volume Handle Finder
to
locate and correct handles, correct handles along one axis at a
time. When you
think the listed handles have been fixed, press the Search For Handles push button
again to verify that no new
handles were created and handles were corrected. Once no handles
are reported
for an axis, search along a different axis and correct the handles
found. The Volume Handle
Finder Dialog is not
guaranteed to find all handles so it may be necessary to inspect a
surface,
such as the inflated surface, for handles.
Once
all of the handles have been corrected, the segmentation volume should
be
saved.
- Select Save Data File from the File Menu.
- Set the
File type to Volume File – AFNI (*.HEAD).
- In the bottom of the Save Parameters Dialog, set the Volume Type to Segmentation.
- Set the
Volume File to the
“ErrorCorrected” segmentation volume that was just edited.
- In the Comment
section, add
information that errors were corrected.
- Change
the name of the volume file from
Human.case9.R.Segment_ErrorCorrected.<date>.HEAD to
Human.case9.R.Segment_ErrorCorrected_fix1.<date>+orig.HEAD.
- Press
the Save push button
to save the error corrected segmentation volume file.
Since
the segmentation volume has been modified to correct topological
errors, the
surface needs to be regenerated.
- Select SureFit Operations (Segmentation) from
the Volume Menu.
- On the Subject
Information Page, just press
the Next push button
since the subject information is already loaded into the page.
- On the Spec
File Selection Page, just press the Next push button since the spec
file is already set.
- On the Volume
Selection Page, set the Volume
Type to Segmentation and the Volume File to the Segmentation Volume File that
was just edited and saved so that the Volume Selection Page appears
like that in Figure 34. Press
the Next push button.

Figure 34
- SureFit Operations Volume Selection (Segmentation Volume)
- On the Volume
Attributes Page, just press
the Next push button.
- The Segmentation
Operations Page has some of its operations disabled (in a
light shade of gray and not responsive to the mouse). These
options are disabled since we are starting with a segmentation volume
instead of an anatomical volume. Deselect Automatic Error Correction since
that process has already been performed. Verify that Generate Raw and Fiducial Surfaces,
Generated Inflated Surface,
Generate Very Inflated Surface,
Generate Ellipsoid Surface,
Create Curvature, Depth, and
Paint Attributes, and Auto
Save Generated Data Files are selected as shown in Figure
35. Press the Next push button to generate all
of the surface and the surface attribute files. Select OK on the Information Dialog informing you
that previously generated surfaces and related files will be
deleted. In the Partial
Hemisphere Padding Dialog, leave all options deselected
and press the OK
button. If you were to segment a partial hemisphere, selections
are made in the Partial Hemisphere
Padding Dialog to inform the surface generation algorithm
where the hemisphere was cut. Generating the surfaces and related
files may take a half hour or more depending upon your computer’s speed.

Figure 35
- Segmentation Operations Page (Final Surfaces)
- Press
the Close push button
on the SureFit Segmentation
Operations dialog.
- Press
the D/C button in the Main Window’s Toolbar to display
the Display Control Dialog.
- Set the
Display Control Dialog
to display the Overlay/Underlay –
Surface page.
- Set the
Underlay to Shape
with Depth as the
selected column.
- View
the different surfaces in the Main
Window.
- Set the
selected Shape column
to Folding (Mean Curvature).
- View
different surfaces with curvature shading the surface.
Now
that the ellipsoid surface has been generated it is time to flatten the
surface.
- Set the
Main Window so that
it displays the Ellipsoid
Surface.
- Select Flatten Full or Partial Hemisphere
from the Surface Menu.
- On the Flatten
Full or Partial Hemisphere Dialog, set the Flattening Type to Full Hemisphere
(Ellipsoid) and Morph Sphere.
- Since Caret5 starts with a volume whose
origin is at the anterior commissure and Caret5 produces surface with
the origin at the anterior commissure, the Anterior Commissure Position
should be set to (0, 0, 0).
- Set the
Border Template Cuts to
Human Right Standard Cuts.
- The Flatten
Full or Partial Hemisphere Dialog should appear as in
Figure 36. Press
the OK button to start
the flattening process. A dialog will pop up asking you to
confirm that the anterior commissure is at the origin. Press the Yes, Continue Flattening push
button.

Figure 36
- Flatten Full Hemisphere Dialog
For a
very thorough description of drawing the borders for flattening (and
registration) visit the web page http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html.
After
a short time the “compressed medial wall” surface will appear with a
red border
somewhat enclosing the medial wall region and blue borders showing
where cuts will
be made. See Figure 37.

Figure 37
- Template Cuts on Compressed Medial Wall Surface
- Drag
the Continue Flattening Full
Hemisphere Dialog to the side.
- Select Viewing Window 2 from the Window Menu.
- Use the
Model Selection Control
in Viewing Window 2 to
view the INFLATED
surface. It may also be helpful to enlarge Viewing Window 2.
- Switch
to a medial View in Viewing Window
2 by pressing
the M button in the Toolbar.
- Press
the View button in the Main Window Toolbar to make sure
that Caret is in View Mode.
- Click
the mouse (perform Node Identification operations) around the boundary
of the inflated surface’s medial wall. The green node
identification symbols will appear on both the inflated and compressed
medial wall surface.
- After identifying the boundary of the medial
wall, identify the calcarine sulcus so that the inflated surface
appears as in Figure 38 and the compressed medial wall surface appears
as in Figure 39.

Figure 38
- Identifying Medial Wall and Calcarine on Inflated Surface in Medial
View

Figure 39
- Identified Medial Wall and Calcarine Cut on Compressed Medial Wall
Surface
- Select Delete Border With Mouse from
the Borders sub-menu of
the Layers Menu. Click the mouse over the
existing medial wall and calcarine borders to delete them.
- Select Draw Border from the Borders sub-menu of the Layers Menu to display the Draw Borders Dialog.
- Press
the Select push button
and in the Name Selection Dialog
highlight MEDIAL.WALL with the mouse and press the OK push button.
- Press
the Apply push button
on the Draw Borders Dialog.
- In the Main
Window, move
the mouse over one of the green symbols around the medial wall. Hold down the left mouse button
and follow the green
symbols to trace out the medial wall. When the mouse gets near
the start of the new border, release
the left mouse button, hold down
the shift key, and click
the left mouse button to tell Caret5 that you are done drawing the
medial wall border.
- In the Draw
Border Dialog, press
the Select push
button. In the Name
Selection Dialog highlight Calcarine Cut and press the OK push button.
- Press
the Apply push button
on the Draw Border Dialog.
Now use the mouse to draw a border along the calcarine sulcus. Be
sure that the border denoting the calcarine sulcus crosses the medial
wall boundary. So, start
drawing the border inside the medial wall and continue to
the posterior part of the calcarine sulcus. The new medial wall
and calcarine sulcus borders should appear similar to that in Figure 40.
- Press
the Close push button
on the Draw Borders Dialog.
- Press
the Close push button
on Viewing Window 2.
- Press
the Continue Flattening
push button on the Continue
Flattening Full Hemisphere Dialog. This next process
will take several minutes.

Figure 40
- Corrected Medial Wall and Calcarine Cut on Compressed Medial Wall
Surface
The
initial flat surface will appear similar to that in Figure 41.
The green symbols may be removed by selecting Clear Node Identify
Symbols from the Identify sub-menu of the Surface Menu or by pressing
the CID button in the Identify Window’s Toolbar. If there are any
large regions
of crossovers (shown in red), indicating handles that are still present
in the
surface, it may be necessary to go back and edit the segmentation
volume to
correct the handles. If the handles are found the edge of the
flat surface
they can be removed by following the instructions in the Initial
Flattening
Dialog.

Figure 41
- Initial Flat Surface
- Continue the flattening process by pressing
the Continue Flattening
push button on the Initial
Flattening Dialog.
- The Multiresolution
Morphing – Flat Dialog will appear. This dialog
contains the parameters that will be used by the multi-resolution
morphing algorithm. This algorithm will reduce distortions in the
flat surface caused by flattening. It rarely necessary to alter
these parameters so just press
the OK push button.
- The Multiresolution
Morphing – Sphere Dialog will appear. This contains
parameters for the reducing the distortion in the spherical
surface. Press
the OK push button to
continue. The multi-resolution morphing of the flat and spherical
surfaces will take a half-hour or longer to complete.
When
the multi-resolution morphing process is complete, several dialogs will
pop
up.
- Drag
the Align Surfaces Dialog
to the side.
- The Spherical
Morphing Measurements Dialog displays measurement
information collected during spherical morphing. Press the Close push button to remove it.
- The Flat
Morphing Measurements Dialog displays measurement
information collected during flat morphing. Press the Close push button to remove it.
- Press
the D/C button in the Main Window Toolbar to display
the Display Control Dialog.
- Change
to the Overlay/Underlay – Surface
Page.
- Set the
Underlay to Shape.
- Set the
Shape column to Folding (Mean Curvature).
- Set the
Primary and Secondary Overlays to No Coloring.
- Press
the Close push button
on the Display Control Dialog
to remove it.
- Place
the Align Surface(s) to Standard
Orientation Dialog to the side of the Main Window.
- Press
the Reset push button
on the Align Surface(s) to
Standard Orientation Dialog.
- In the Main
Window, click
the mouse on the ventral tip of the Central Sulcus (near the middle of
the surface) The ventral tip is shown by the green square in near the
center of Figure 42.

Figure 42
- Unaligned Flat Surface
- Hold down
the Shift Key and click
the mouse on the dorsal-medial tip of the Central Sulcus (opposite end
of the Central Sulcus from click made in last step). You should
see X and Y values for the Ventral and Dorsal-Medial Tips of the
Central Sulcus in the Align
Surface(s) to Standard Orientation Dialog.
- In the Spherical
Surface section of the Align
Surface(s) to Standard Orientation Dialog, check the box to the left of Align Sphere.
- Press
the Apply push button
on the Align Surface(s) to
Standard Orientation Dialog. After a short time the
flat surface should appear similar to Figure 43.
- Press
the Close push button
on the Align Surface(s) to
Standard Orientation Dialog.

Figure 43
- Aligned Flat Surface
Since
data files (flat coordinate, spherical coordinate, and latitude
longitude) have
been modified by the alignment process, they need to be saved.
- Select Save Data File from the File Menu.
- Set the
File type to Coordinate Files (*.coord).
- Near the bottom of the dialog verify that Coord File is the
CYCLE5_OVERLAP_SMOOTH coordinate file.
- Set the
Coord Frame to Cartesian Standard.
- Set the
Orientation to Left, Posterior, Inferior.
- Add
information about alignment to standard orientation to the Comment section.
- Change
the File name to
Human.case9.R.FLAT_ALIGNED.<date>.<#nodes>.coord so that
the dialog is similar to that in Figure 44.

Figure 44
- Save Aligned Flat Coordinate File
- Press
the Save push button to
save the file.
- Select Save Data File from the File Menu.
- Near the bottom of the dialog set the Coord File to the SPHERE_CYCLE4
coordinate file.
- Set the
Coord Frame to Spherical Standard.
- Set the
Orientation to Left, Posterior, Inferior.
- Change
the File name to
Human.case9.R.SPHERE_ALIGNED.<date>.<#nodes>.coord.
- Press
the Save push button to
save the file.
- Select Save Data File from the File Menu.
- Set the
File type to Latitude Longitude Files (*latlon).
- Change
the File name to
Human.case9.R.LAT_LON.<date>.<#nodes>.latlon.
- Press
the Save push button to
save the file.
At
this point you are done.
* Select
Exit
from the File Menu (Quit from the Caret Menu for Macintosh
users).
Caret5
provides two registration methods, flat and spherical, for bringing one
surface
into register with another using landmarks to constrain the
deformation. The
landmarks consist of borders that identify regions identified on both
surfaces
such as the medial wall boundary and various sulci. There are
several
advantages of spherical registration over flat registration.
First, the
spherical surfaces are closed (contain no cuts), eliminating the
requirement
for landmarks along the surface perimeter in flat registration.
Secondly,
spherical registration requires six landmarks, two along the medial
wall
boundary, and one each on the calcarine sulcus, the central sulcus, the
sylvian
fissure, and the superior temporal gyrus.
The
first step in performing a spherical registration is to draw the needed
registration landmarks (borders) on both the individual and atlas
surfaces.
For good quality registration, six registration landmarks are
needed.
Fortunately, three of the six required registration landmarks are
automatically
created during the flattening of a full hemisphere. You may
recall drawing the
medial wall and calcarine cuts during the flatten full hemisphere
process. The
medial wall cut becomes two of the registration landmarks by splitting
it into
two pieces where it intersects both the frontal and calcarine
cuts. The
calcarine cut becomes the third registration landmark. You will
need to draw
the other three required registration landmarks that denote the central
sulcus,
the sylvian fissure, and the superior temporal gyrus.
For a
very thorough description of drawing the borders for registration (and
flattening)
visit the web page http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html.
There
are two other very important considerations regarding the landmark
borders.
First, both the individual and atlas landmarks must consist of the same
number
of borders with a one-to-one correspondence in the border names.
Secondly,
each of the corresponding landmark borders must be oriented in the same
manner. In other words, each of the corresponding borders must
begin and end
in corresponding anatomical locations.
- Exit
out of any Caret5 programs that are running.
- Change
into the tutorial’s registration/INDIVIDUAL.1582.L
directory.
- Start
Caret5.
- Open
the Human.1582.L.REGISTER-with-ATLAS.03-05.65950.spec
specification file.
- In the spec file dialog press the Select All
button, deselect both
of the border projection files, and press the Load button to load the
files.
- In the Main Window, use the Model Selection Control
to select the FLAT
surface.
- Press
the Toolbar:D/C
button to launch the Display Control Dialog.
- On the Overlay/Underlay – Surface
panel, set Shape to Folding – Fiducial –
1582L to see the folding (mean curvature) on the flat
surface.
- Select Layers: Borders: Draw
Border to launch the Draw Border Dialog.
- Press
the Select
button in the Draw
Borders Dialog’s Attributes frame.
- Select
the name LANDMARK.CentralSulcus and press the OK button in the Name Selection Dialog.
- Set the
Resampling
to 4.0.
- Verify that the Type is
set to Open.
- Press
the Apply
in the Draw
Borders Dialog.
- Draw a
border that follows the fundus of the central sulcus. Be sure to
start at the bottom of the central sulcus near the middle of the window
and draw upwards to the other end of the central sulcus (yellow border
in Figure 46). If you do not know how to draw a border, see the
borders section of this document.
- Press
the Select
button in the Draw
Borders Dialog.
- In the Name Selection Dialog, choose the
LANDMARK.SylvianFissure item and press
the OK
button to close the Name Selection Dialog.
- Draw a
border that follows the sylvian fissure. Start at the end of the
sylvian fissure near the middle of the surface and draw left and down
as show in Figure 46.
- Use the
Main Window’s
Model Selection Control to view the INFLATED surface.
- Press
the Main Window
Toolbar’s View button to place the mouse back into view
mode.
- Use the
ID Node function to identify (click
the mouse) along the anterior portion of the superior temporal gyrus.

Figure 44 - Node Identified
Along Superior Temporal
Gyrus
- Use the
Main Window’s
Model Selection Control to return to viewing the FLAT
surface.
- Press
the Selection
button in the Draw
Borders Dialog.
- In the Name Selection Dialog, choose the LANDMARK.SF_STSant
item and press the OK button
to close the Name
Selection Dialog.
- Press
the Draw Borders
Dialog’s Close button.
- Starting at the top of the identified nodes, draw superior temporal gyrus
border.
- Switch
the Display
Control Dialog to the Border panel.
- In the Main tab, select Show First Link Red.
You will see the beginning of each border in red as in Figure 46.

Figure
46 - Central Sulcus, Superior Temporal Gyrus, and
Sylvian
Fissure Landmarks
- Select Layers: Borders:
Project Borders. Leave the Projection Method set to Nearest Tile
and press the OK button
in the Border
Projection Dialog. This will project the three
borders that you have just drawn to all of the other surfaces.
- Use the Model Selection Control to view the SPHERICAL surface in the Main Window.
Rotate the surface
to view the Central Sulcus landmark (in yellow) and the Sylvian Fissure
landmark (in cyan).
- Press
the Spec
button in the Main
Window Toolbar.
- Press
the Open
button to the left of the border projection file
Human.1582.L.Full.LANDMARKS.FromFlattening.65960.borderproj. In
the Append or
Replace Dialog, choose
Append.
This loads the landmarks that were automatically created when the
hemisphere was flattened.
- In the Main Window’s Toolbar, press the M button to get a medial
view of the spherical surface. You will see additional landmarks
around the medial wall and along the calcarine sulcus (Figure 46).

Figure
46 - Landmarks on Flat

Figure 47 - Landmarks on Sphere
- Choose File: Save Data File.
- In the Save Data File Dialog, set the File Type to Border Projection Files.
- In the File Name text box, change the name to
Human.1582.L.Full.LANDMARKS.ForSphericalRegistration.65950.borderproj.
- Press
the Save
button to save the border projection file.
- Exit
out of this Caret program. You will be informed about unsaved
border files that were created during the border projection
process. We do not need these since the border projection file
was saved, so, quit without saving.
The
INDIVIDUAL surface now has the landmarks required for
registration. The ATLAS
surface already has its needed landmarks so it is now time to execute
the
registration process.
- Change
up one directory level so that you are in the tutorial’s
REGISTER_SPHERE directory.
- Start
Caret5.
- Select Surface: Deformation:
Run Spherical Surface Deformation to launch the Spherical Surface
Deformation Dialog.
- Press
the Individual
Tab.
- Press
the Spec File
button.
- In the Choose Spec File Dialog, go into the INDIVIDUAL.1582.L
directory, select the
Human.1582.L.REGISTER-with-ATLAS.03-05.65950.spec specification file,
and press the Open
button. This results in the remaining fields of the dialog being
set.
- Press
the Border File
button. Make sure the selected border file is set to
Human.1582.L.Full.LANDMARKS.ForSphericalRegistration.65950.borderproj.
- Press
the Atlas
tab.
- Press
the Spec File
button.
- In the Choose Spec File Dialog, go into the ATLAS_LEFT_HEM
directory, select the
Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec specification
file, and press the Open
button.
- Press
the Spherical
Parameters tab.
- Press
the Select
Standard Parameters button (near the bottom of the
dialog).
- In the Choose Registration Parameters Dialog,
press the Human to Human
radio button and press
the OK
button.
- Press
the OK
button on the Spherical
Surface Deformation Dialog to start the deformation. This
will take 10 to 20 minutes depending upon the speed of the computer.
- Part way through the deformation process, you
might get a dialog reporting that crossovers (spherical surface
tangles) were encountered. If the number is small (i.e. less than
12) choose to continue the deformation process. If the number is
larger, it is possible that one of the landmarks, central sulcus, or
sylvian fissure was drawn in the wrong orientation. Verify that
the landmarks are correct.
Viewing Registration Results
- Press
the OK
button on the Deformation
Completed Dialog. Exit out of this Caret5.
- Change
into the REGISTER_SPHERE/ATLAS_LEFT_HEM directory.
- Start
Caret5.
- In the Open Spec File Dialog are
two spec files. Choose
the deformation_Human.1582.L.REGISTER-with-ATLAS.03-05.71785.spec which
contains the individual’s data (1582.L) registered to the atlas surface.
- In the Spec File Dialog, in
addition to the default files, select
either of the Area
Color Files, either of the Border Color Files, the
deformed_Human.1582.L.CartesianGrid.71785 Border Projection file, the
deformed_1582.L.Eye-movements-attention.71785.metric Metric file, and both of the
Paint
files. Deselect
the deformed_Human.1582.L.COMPOSITE.71785.surface_shape Surface Shape
file and select the
Human.colin.L.COMPOSITE.71785.surface Surface Shape file. Press the Load button to load the
files.
- In the Main Window, use the Model Selection Control
to view the FLAT
surface. The Cartesian grid borders provide feedback on the
surface deformation.
- Press
the ToolBar:D/C
button to launch the Display Control Window.
- Press
the Borders
button near the bottom to turn off the borders.
- Set the
Primary Overlay
to Paint
and select the Paint
column Geography – 1582.L to see the individual’s sulcal pattern
deformed to the atlas.
- Switch
the Paint
to Geography – Human.colin.L to view the atlas’ geography and contrast
it with the individual’s geography.
- Set the
Primary Overlay
to Metric
to view the individual’s functional data deformed to the atlas.
- Exit
this Caret5.
To
segment at the command line, the volume must be in an LPI orientation
with its
origin set so that the (0, 0, 0) stereotaxic coordinate is at the
anterior
commissure. The gray and white peaks must also be known.
VOLUME
SEGMENTATION
caret_command -volume-segment <operation_code> \
<f-gray-peak> <f-white-peak> \
<padding-code> <structure> <spec-file-name>
<anat-or-segment-volume>
Operation_Code characters
Specify each with either a "Y" or "N".
All characters must be specified.
Character Operation Description
--------- ---------------------
1 Disconnect Eye and Skull
2 Disconnect Hindbrain
3 Use High Threshold for Hindbrain disconnection
4 Cut Corpus Callossum
5 Generate Segmentation
6 Fill Ventricles
7 Automatic Error Correction
8 Generate Raw and Fiducial Surfaces
9 Generate Inflated Surface
10 Generate Very Inflated Surface
11 Generate Ellipsoid Surface (For Flattening)
12 Generate Hull Surface
13 Generate Curvature, Depth, and Paint Attributes
gray-peak specifies the intensity of the gray matter peak in the
anatomy volume.
white-peak specifies the intensity of the white matter peak in the
anatomy volume.
padding-code
Specify padding for any cut faces when segmenting a partial hemisphere.
Specify each with either a "Y" for padding or "N" for no
padding.
All characters must be specified.
Character Padding Description
--------- -------------------
1 Pad Negative X
2 Pad Positive X
3 Pad Posterior Y
4 Pad Anterior Y
5 Pad Inferior Z
6 Pad Superior Z
structure Specifies the brain structure.
Acceptable values are RIGHT or LEFT
spec-file-name Name of specification file.
anat-or-segment-volume Name of input volume.
The volume must be in a Left-Posterior-Inferior orientation and
its
stereotaxic coordinates must be set so that the origin is
at the anterior commissure.