Freesurfer ingress reorient #2199

birajstha · 2025-03-24T19:01:02Z

Fixes

Fixes #2200 by @birajstha
related to #2193 by @tamsinrogers

Alignment issues during applying mask ingressed from Freesurfer outputs.

Description

Resources from ingress_freesurfer are skipping reorient and are used directly like in here.

This causes the files ingressed to have different orientation and is incompatible with rest of the data causing alignment issues such as above.

This PR solves the above issue by aligning the ingressed resources to common orientation.

Technical details

Tests

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After the fix

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shnizzedy

Just a quibble with a comment, otherwise looks great to me!

This is only an issue for ingress, not if we're running FreeSurfer in the pipeline?

CPAC/pipeline/engine.py

Co-authored-by: Jon Cluce <[email protected]>

birajstha · 2025-03-24T20:31:32Z

@shnizzedy , I havent't checked running freesurfer in the pipeline but, we should probably do that as well.
I guess it wont hurt to put a reorient workflow in there just to be safe.

shnizzedy · 2025-03-25T17:40:04Z

I guess it wont hurt to put a reorient workflow in there just to be safe.

I think if we're doing it in both places, we should abstract it to its own node or nodeblock that's included in both flows.

shnizzedy · 2025-03-25T17:40:50Z

CPAC/pipeline/engine.py

+            # reorient *.mgz
+            if outfile.endswith(".mgz"):


These

C-PAC/CPAC/pipeline/engine.py

Lines 2014 to 2018 in 325deb5

"pipeline-fs_raw-average": "mri/rawavg.mgz",

"pipeline-fs_subcortical-seg": "mri/aseg.mgz",

"pipeline-fs_brainmask": "mri/brainmask.mgz",

"pipeline-fs_wmparc": "mri/wmparc.mgz",

"pipeline-fs_T1": "mri/T1.mgz",

need reoriented but these

C-PAC/CPAC/pipeline/engine.py

Lines 2019 to 2035 in 325deb5

"pipeline-fs_hemi-L_desc-surface_curv": "surf/lh.curv",

"pipeline-fs_hemi-R_desc-surface_curv": "surf/rh.curv",

"pipeline-fs_hemi-L_desc-surfaceMesh_pial": "surf/lh.pial",

"pipeline-fs_hemi-R_desc-surfaceMesh_pial": "surf/rh.pial",

"pipeline-fs_hemi-L_desc-surfaceMesh_smoothwm": "surf/lh.smoothwm",

"pipeline-fs_hemi-R_desc-surfaceMesh_smoothwm": "surf/rh.smoothwm",

"pipeline-fs_hemi-L_desc-surfaceMesh_sphere": "surf/lh.sphere",

"pipeline-fs_hemi-R_desc-surfaceMesh_sphere": "surf/rh.sphere",

"pipeline-fs_hemi-L_desc-surfaceMap_sulc": "surf/lh.sulc",

"pipeline-fs_hemi-R_desc-surfaceMap_sulc": "surf/rh.sulc",

"pipeline-fs_hemi-L_desc-surfaceMap_thickness": "surf/lh.thickness",

"pipeline-fs_hemi-R_desc-surfaceMap_thickness": "surf/rh.thickness",

"pipeline-fs_hemi-L_desc-surfaceMap_volume": "surf/lh.volume",

"pipeline-fs_hemi-R_desc-surfaceMap_volume": "surf/rh.volume",

"pipeline-fs_hemi-L_desc-surfaceMesh_white": "surf/lh.white",

"pipeline-fs_hemi-R_desc-surfaceMesh_white": "surf/rh.white",

"pipeline-fs_xfm": "mri/transforms/talairach.lta",

don't, is that right?

Good question ! It looks like all pipeline-fs_hemi* are not used in CPAC but are only ingressed.
I am not sure about pipeline-fs_xfm. It probably needs reorient/resample as well.
I will loop in @sgiavasis here for further clarification.
Steve, do we need to resample this xfm?

We've had extensive conversation on this off of GitHub, but going forward from here, let's resolve whatever requested changes there are and merge this.

For the reorient for running Freesurfer as part of the C-PAC pipeline, let's open a separate but related PR for it, as it will be an extension of this one but different.
I'd like to get some runs going with this change for now (since it will be ingressed).

I am adding this below for documentation purposes.
Tested applying the xfm mentioned above to wmparc from

Freesurfer native orientation

and
2. reoriented one from this PR

There appears to be no difference in the output.

So reorienting only .mgz files.

shnizzedy

So reorienting only .mgz files.

https://github.com/FCP-INDI/C-PAC/pull/2199/files#r2035560042

If that's what we're doing, then I think this PR's good to go.

birajstha · 2025-04-09T15:15:29Z

Thanks for the review. I also added #2208 to follow up with your comment on adding reorientation to the FS outputs when ran natively with CPAC.

with precommit

2f514ca

github-project-automation bot added this to C-PAC Development Mar 24, 2025

birajstha temporarily deployed to ACCESS March 24, 2025 19:01 — with GitHub Actions Inactive

Merge branch 'develop' into fs_ingress_reorient

0b2a017

birajstha requested a review from a team March 24, 2025 19:02

correcting the function doc-string

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shnizzedy requested changes Mar 24, 2025

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birajstha linked an issue Mar 24, 2025 that may be closed by this pull request

🐛Freesurfer output data skips reorientation #2200

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Update CPAC/pipeline/engine.py

325deb5

Co-authored-by: Jon Cluce <[email protected]>

shnizzedy reviewed Mar 25, 2025

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Merge branch 'develop' into fs_ingress_reorient

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shnizzedy approved these changes Apr 9, 2025

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birajstha mentioned this pull request Apr 9, 2025

🐛 Add reorientation to the Freesurfer outputs when ran within CPAC. #2208

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birajstha requested a review from sgiavasis April 9, 2025 15:52

sgiavasis approved these changes Apr 9, 2025

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sgiavasis merged commit 2ffff67 into develop Apr 9, 2025
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github-project-automation bot moved this to ✅ Done in C-PAC Development Apr 9, 2025

birajstha deleted the fs_ingress_reorient branch April 10, 2025 15:08

	"pipeline-fs_raw-average": "mri/rawavg.mgz",
	"pipeline-fs_subcortical-seg": "mri/aseg.mgz",
	"pipeline-fs_brainmask": "mri/brainmask.mgz",
	"pipeline-fs_wmparc": "mri/wmparc.mgz",
	"pipeline-fs_T1": "mri/T1.mgz",

	"pipeline-fs_hemi-L_desc-surface_curv": "surf/lh.curv",
	"pipeline-fs_hemi-R_desc-surface_curv": "surf/rh.curv",
	"pipeline-fs_hemi-L_desc-surfaceMesh_pial": "surf/lh.pial",
	"pipeline-fs_hemi-R_desc-surfaceMesh_pial": "surf/rh.pial",
	"pipeline-fs_hemi-L_desc-surfaceMesh_smoothwm": "surf/lh.smoothwm",
	"pipeline-fs_hemi-R_desc-surfaceMesh_smoothwm": "surf/rh.smoothwm",
	"pipeline-fs_hemi-L_desc-surfaceMesh_sphere": "surf/lh.sphere",
	"pipeline-fs_hemi-R_desc-surfaceMesh_sphere": "surf/rh.sphere",
	"pipeline-fs_hemi-L_desc-surfaceMap_sulc": "surf/lh.sulc",
	"pipeline-fs_hemi-R_desc-surfaceMap_sulc": "surf/rh.sulc",
	"pipeline-fs_hemi-L_desc-surfaceMap_thickness": "surf/lh.thickness",
	"pipeline-fs_hemi-R_desc-surfaceMap_thickness": "surf/rh.thickness",
	"pipeline-fs_hemi-L_desc-surfaceMap_volume": "surf/lh.volume",
	"pipeline-fs_hemi-R_desc-surfaceMap_volume": "surf/rh.volume",
	"pipeline-fs_hemi-L_desc-surfaceMesh_white": "surf/lh.white",
	"pipeline-fs_hemi-R_desc-surfaceMesh_white": "surf/rh.white",
	"pipeline-fs_xfm": "mri/transforms/talairach.lta",

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Freesurfer ingress reorient #2199

Freesurfer ingress reorient #2199

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