table of contents
LIPSIA     Conversion of NIfTI-1 images to the Vista format
niftov

The program 'niftov' converts NIfTI-1 images into vista. The following data types are allowed: anatomical data (ubyte or short), functional data (short), and statistical or parametric maps (float).

niftov -in niftiimage.nii -out vistaimage.v

For converting functional data, the repetition time (TR) must be specified:

niftov -in functional3D.nii -out functional3D.v -tr 2

Important: In Lipsia, raw functional slices (i.e. before preprocessing) must be ordered from ventral to dorsal (i.e. upside down). Therefore, for (2D-)functional raw data, the correct command line is:

niftov -in functional.nii -out functional.v -tr 2 -zflip true

To do a correct data conversion from the NIfTI to the Lipsia data format, please read the chapters 'The Lipsia data format' and 'How to convert data into the Lipsia data format'.

The converter 'niftov' does not put slicetime information into the header of the resulting vista file. If a slicetime correction should be performed with an output of 'niftov', the slicetime information must be specified in a text-file before using 'vslicetime'.

vtonifti

'vtonifti' can be used to convert Lipsia data into the NIfTI data format. The orientation of the image is written into the NIfTI header. For manual flipping, the command-line options 'xflip', 'yflip', and 'zflip' can be used.

Note that the affine coordinate definitions are not yet implemented in both programs 'niftov' and 'vtonifti'.

More information about NIfTI and sample data can be found via nifti.nimh.nih.gov.

Parameters of 'niftov':
-help
Prints usage information.
-in
NIfTI-1 input file. Required.
-out
Output file. Default: (none)
-precision auto | original
precision of anatomical data. Default: auto
-black
lower histogram cutoff for contrast scaling. Default: 0.1
-white
upper histogram cutoff for contrast scaling. Default: 0.1
-xflip
[ true | false ] Flip x axis. Default: true
-yflip
[ true | false ] Flip y axis. Default: false
-zflip
[ true | false ] Flip z axis. Default: false
-tr
repetition time in seconds. Default: 0
-orientation
axial | sagittal | coronal Orientation of slices. Default: axial
Parameters of 'vtonifti':
-in
Input file. Default: (none)
-out
Output stub. Required.
-xflip
[ true | false ] Flip x axis. Default: true
-yflip
[ true | false ] Flip y axis. Default: false
-zflip
[ true | false ] Flip z axis. Default: false


Max Planck Institute for Human Cognitive and Brain Sciences. Further Information: lipsia@cbs.mpg.de
Copyright © 2007 Max Planck Institute for Human Cognitive and Brain Sciences. All rights reserved.