atlastool
Description:
A utility to manipulate nifti atlas files
Inputs:
A template file which is either a 3D NIFTI with different regions specified by integer values, or a 4D NIFTI with nonzero values indicating that a voxel is in the region indicated by the 4th dimension.
Outputs:
A new NIFTI template file which has been processed using the options specified
Usage:
A utility to manipulate nifti atlas files
usage: atlastool [-h] [--3d] [--4d] [--split] [--maskthresh FILE]
[--labelfile FILE] [--xfm FILE] [--targetfile TARGETFILE]
[--maskfile MASK] [--removeemptyregions] [--RtoL] [--debug]
[--maxval MAXVAL]
inputtemplatename outputtemplatename
Positional Arguments
- inputtemplatename
Input NIFTI file name. Must be either a 3D file with different regions specified by integer values, or a 4D file with nonzero values indicating that a voxel is in the region.
- outputtemplatename
Output NIFTI file name.
Named Arguments
- --3d
Return a 3d file with regions encoded as integers
Default: False
- --4d
Return a 4d file with one region per volume
Default: False
- --split
Split regions along the midline into left and right subregions
Default: False
- --maskthresh
Threshhold for autogenerated mask (default is 0.25).
Default: 0.25
- --labelfile
Labels for the source atlas
- --xfm
Transform file to go to the reference.
- --targetfile
Match the resolution of TARGET
- --maskfile
Mask the final atlas with the 3D mask specified (if using a target file, mask must match it).
- --removeemptyregions
Remove regions with no voxels, so that label values are consecutive. Adjust the label file as necessary.
Default: False
- --RtoL
Reverse left/right assignment of labels (default is LtoR). Change if the default output is wrong.
Default: True