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[RTM] ENH: Register FreeSurfer template to FMRIPREP template #733

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Merged
merged 7 commits into from
Oct 8, 2017
Merged

[RTM] ENH: Register FreeSurfer template to FMRIPREP template #733

merged 7 commits into from
Oct 8, 2017

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effigies
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@effigies effigies commented Oct 2, 2017 •
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Addresses issue raised in #726 (comment).

Given this, I think we should output the registration transform, to give users the tools to move between FMRIPREP and FreeSurfer spaces. I'd recommend the LTA format, since that has more metadata about the source and target spaces; if users need to convert to other formats, they will presumably have access to the LTAConvert tool.

To do:

  • Ensure output surfaces are aligned with T1_preproc
  • Affine

@effigies effigies force-pushed the fix/freesurfer_register branch 2 times, most recently from 70510d2 to b7376f0 Compare October 4, 2017 23:29
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effigies commented Oct 5, 2017

Addressing this approach to BEP 014, I believe what we'll want is:

fmriprep/sub-<label>/anat/sub-<label>_T1w_preproc_target-fsnative_affine.txt

In which case, we want the inverse of what I'm currently generating, which is easily constructed with

lta_convert --inlta transform.lta --outitk transform.txt --invert

I think the most appropriate alternative would be to add a transform to the freesurfer/sub-<label>/mri/transforms/ directory, and I feel we should make minimal changes there.

@effigies effigies force-pushed the fix/freesurfer_register branch 2 times, most recently from f4a03f3 to db69910 Compare October 5, 2017 18:37
@effigies effigies mentioned this pull request Oct 5, 2017
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@effigies effigies force-pushed the fix/freesurfer_register branch 4 times, most recently from a57b762 to 155812c Compare October 6, 2017 14:38
This was referenced Oct 6, 2017
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@effigies effigies force-pushed the fix/freesurfer_register branch 3 times, most recently from 5476457 to 4f22e86 Compare October 6, 2017 18:49
@effigies effigies changed the title [WIP] ENH: Register FreeSurfer template to FMRIPREP template [RTM] ENH: Register FreeSurfer template to FMRIPREP template Oct 6, 2017
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effigies commented Oct 6, 2017

To review this PR, separately review #741, and then look at effigies/fmriprep@fsfix_common...fix/freesurfer_register.

@effigies effigies force-pushed the fix/freesurfer_register branch 2 times, most recently from 2c74d20 to 0a3adce Compare October 6, 2017 20:14
oesteban
oesteban approved these changes Oct 6, 2017
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Everything seems reasonable, with the constraints of my limited knowledge about surfaces in freesurfer.

.circle/data/ds005_outputs.txt Outdated
@@ -24,6 +24,7 @@ ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-WM_pro
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_warp.h5
ds005/out/fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
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I thought the filename was sub-01_T1w_preproc_target-fsnative_affine.txt (missing _preproc)

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I did change it to make it more like ds005/out/fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_warp.h5, which is a transform from T1w space to MNI152NLin2009cAsym. Speaking of which, @chrisfilo, reading the BEP, should that be a target-MNI... instead of space-MNI...?

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Correct.

fmriprep/interfaces/surf.py
@@ -218,3 +224,20 @@ def normalize_surfs(in_file):
pointset.meta.data.insert(2, geom_type)
img.to_filename(fname)
return os.path.abspath(fname)


def load_transform(fname):
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a minimal docstring here?

@effigies effigies force-pushed the fix/freesurfer_register branch 3 times, most recently from 47fa78a to 0b153ec Compare October 7, 2017 13:42
@effigies effigies force-pushed the fix/freesurfer_register branch from 0b153ec to 9ed6a6e Compare October 7, 2017 17:07
@oesteban oesteban merged commit 2a2ac71 into nipreps:master Oct 8, 2017
@effigies effigies deleted the fix/freesurfer_register branch October 8, 2017 16:32
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@effigies @chrisgorgo @oesteban