Flag

Description

--inm3z <in.m3z>

input M3Z warp

--inmgzwarp <inwarp.mgz>

input mgz warp (Freesurfer 3D morph in mgz format)

--infsl <in.nii.gz>

input FSL warp (recommend to use with --insrcgeom)

--inspm <y_rinput.nii>

input SPM warp (use use with --insrcgeom), data format is either abs-ras (default) or abs-crs (use --inwarpformat to specify)

--inlps, --initk <in.nii.gz>

input LPS-to-LPS displacement field (e.g. ITK, ANTs)

--inras <in.nii.gz>

input RAS-to-RAS displacement field (e.g. NiftyReg)

--invox <in.mgz>

input file with displacements in source-voxel space

Flag

Description

--outm3z <out.m3z>

output warp (M3Z Freesurfer format)

--outmgzwarp <outwarp.mgz>

output mgz warp (Freesurfer 3D morph in mgz format)

--outfsl <out.nii.gz>

output warp (FSL format)

--outlps, --outitk <out.nii.gz>

output LPS-to-LPS displacement field (e.g. ITK, ANTs)

--outras <out.nii.gz>

output RAS-to-RAS displacement field (e.g. NiftyReg)

--outvox <out.mgz>

output file with displacements in source-voxel space

Flag

Description

-g or --insrcgeom <geom.mgz>

Specify volume geometry of the input to the warp space, i.e., srcgeom shares an RAS space with the warp volume. Usually this is identical to the geom of the warp volume itself (if the warp input is in a format that has such info). This also allows the input to the warp to have a different geometry than the warp itself, though this is probably better handled with -lta1.

-d or ---downsample

Downsample output M3Z to spacing of 2.

-lta2 LTA (or -lta2-inv)

Create composite morph for warping a source image -> LTA1 -> GCAM -> LTA2 -> atlas/destination image

--inwarpformat inwarp-format

specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs)

--outwarpformat outwarp-format

specify warp data format: abs-crs, disp-crs, abs-ras, or disp-ras (default is abs-crs)

--vg-thresh vgthresh

threshold for testing diffs in volume geom