Fixing ccs options brain masking

[birajstha]

Fixes

Fixes

• 🐛 Change output names of Freesurfer FSL ccs-options brain masking outputs #2263 by @sgiavasis
• 🐛 Repair Freesurfer FSL ccs-options brain mask workflow #2266 by @sgiavasis

Description

Modified ccs-options Tight/Loose brain mask generation nodeblocks to name the masks appropriately so that it moves downstream to the rest of pipeline and can be used in brain extraction as swappable T1w brain masks.

Technical details

Converts the tight/loose brain masks into generic mask that can be used downstream.

outputs["space-T1w_desc-brain_mask"] = outputs.pop("space-T1w_desc-loose_brain_mask")

Adding metadata info into the nodeblock decorator as

    outputs={
        "space-T1w_desc-brain_mask": {
            "Description": "Brain mask extracted using FreeSurfer-BET-Loose method",
            "Method": "FreeSurfer-BET-Loose",
            "Threshold": "loose"
        }

Tests

Run CPAC with config where these brain extraction methods are enabled and then see if the respective outputs are available in the output/anat dir.

anatomical_preproc:
  run: On
  brain_extraction:
    run: On
    using: [FreeSurfer-BET-Tight, FreeSurfer-BET-Loose]

Screenshots

Ran Config with

and checked the output/anat

CPAC Variant info in the metadata

Final Masked Brain from Tight (left) Loose (right)

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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[codecov]

Codecov Report

Attention: Patch coverage is 97.14286% with 1 line in your changes missing coverage. Please review.

Project coverage is 28.8%. Comparing base (e2d6a31) to head (266f7a4).

Files with missing lines	Patch %	Lines
CPAC/anat_preproc/anat_preproc.py	66.7%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           develop   #2265     +/-   ##
=========================================
+ Coverage     28.7%   28.8%   +0.1%     
=========================================
  Files          230     230             
  Lines        26169   26195     +26     
  Branches      4113    4113             
=========================================
+ Hits          7503    7541     +38     
+ Misses       18018   18006     -12     
  Partials       648     648             

Files with missing lines	Coverage Δ
CPAC/anat_preproc/tests/test_anat_preproc.py	41.3% <100.0%> (+24.4%)	⬆️
CPAC/anat_preproc/anat_preproc.py	12.4% <66.7%> (+0.7%)	⬆️

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[shnizzedy]

I think as long as clearing

C-PAC/CPAC/anat_preproc/anat_preproc.py

Lines 1350 to 1366 in e2d6a31

	# CCS brain mask is in FS space, transfer it back to native T1 space
	fs_fsl_brain_mask_to_native = pe.Node(
	interface=freesurfer.ApplyVolTransform(),
	name=f"fs_fsl_brain_mask_to_native_{node_id}",
	)
	fs_fsl_brain_mask_to_native.inputs.reg_header = True
	fs_fsl_brain_mask_to_native.inputs.interp = "nearest"
	wf.connect(
	binarize_combined_mask, "out_file", fs_fsl_brain_mask_to_native, "source_file"
	)
	node, out = strat_pool.get_data("pipeline-fs_raw-average")
	wf.connect(node, out, fs_fsl_brain_mask_to_native, "target_file")
	node, out = strat_pool.get_data("freesurfer-subject-dir")
	wf.connect(node, out, fs_fsl_brain_mask_to_native, "subjects_dir")

out is intentional then this looks good.

[shnizzedy]

Since this PR is recent and ccs-options masking, I wonder if this change is causing #2279?

[birajstha]

Since this PR is recent and ccs-options masking, I wonder if this change is causing #2279?

@shnizzedy , yeah looks like it. It seems like the subjects I ran tests with had same image for FS and T1w space so it passes all my tests. Will look into this

[birajstha]

Oh I remember why we removed that step. It produced a noise.