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Hi all!
I am working on implementing some freesurfer synth tools into a larger
diffusion processing pipeline. Doing so, I would like to use mri_synthmorph to
generate a transform and then pass it downstream. FIrstly, I use the dockerized
synthmorph version, which seems to present discrepancies in its behaviour vs
local testing:
1.
Can someone explain the expected output format of freesurfer transforms? When
used within docker, I must define affine transforms as .lta and deform
transforms as .mgz, otherwise: "ValueError: cannot determine file format from
extension for test__init_warp.txt"; while when using mri_synthform from my
local freesurfer installation, it doesn't seem like an issue. While I expected
.m3z to be the expected output.
2.
Here is the sequence of functions I use. My objective is to pass down the
resulting transform (affine initialization + deform warp) downstream my
pipeline for further registration using ANTs (antsApplyTransforms). I tested
and it seems to work, but i would appreciate an opinion. Does the --insrcgeom
parameter fixes everything for me?
*
Initialization + registration (freesurfer):
*
mri_synthmorph -m affine -t <init.lta> [moving] [fixed]
mri_synthmorph -m deform -t <freesurfer_warp.mgz> -o <warped.nii.gz> -i
<init.txt> [moving] [fixed]
Convert warp from freesurfer (RAS) to ANTs (LPS) using freesurfer warp_convert:
mri_warp_convert -g [moving] --inras <freesurfer_warp.mgz> --outlps
<ants_warp.nii.gz>
Thank you very much!
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