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