Freesurfer ingress reorient

[birajstha]

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

Screenshots

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?

[birajstha]

@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]

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]

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?

[birajstha]

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?

[sgiavasis]

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).

[birajstha]

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

1. Freesurfer native orientation

and
2. reoriented one from this PR

There appears to be no difference in the output.

[birajstha]

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]

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.