Fixing bold-T1w-Template registration in abcd-options preconfig

[birajstha]

Fixes

Related to #2274, #2275 ,

Description

This PR resolves the bold-to-T1w-to-Template registration issue, that was causing cropped image and some non brain areas in the bold processing pipeline.

Technical details

This PR refactors the transform_timeseries_to_T1template_abcd nodeblock, removing few unnecessary nodes and changing reference inputs to the registration node.
Adds a node to match FOV between T1w and Template, the transform is concatenated to the XFM, which later is used in the above nodeblock for bold-to-T1w-to-Template registration.

Tests

Tested running abcd-options preconfig.
A report from shortened abcd-options pipeline attached
sub-NDARINV003RTV85_ses-baselineYear1Arm1_qc_report.pdf

Screenshots

Before

After

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
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• 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

❌ Patch coverage is 80.55556% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 34.0%. Comparing base (83e4c7a) to head (fb7e86f).
⚠️ Report is 20 commits behind head on develop.

Files with missing lines	Patch %	Lines
CPAC/registration/registration.py	80.6%	3 Missing and 3 partials ⚠️
CPAC/pipeline/cpac_pipeline.py	66.7%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           develop   #2276   +/-   ##
=======================================
  Coverage     34.0%   34.0%           
=======================================
  Files          233     233           
  Lines        26341   26304   -37     
  Branches      4127    4130    +3     
=======================================
- Hits          8954    8953    -1     
+ Misses       16666   16620   -46     
- Partials       721     731   +10     

Files with missing lines	Coverage Δ
CPAC/func_preproc/func_preproc.py	26.1% <100.0%> (ø)
CPAC/pipeline/schema.py	84.1% <ø> (ø)
CPAC/pipeline/cpac_pipeline.py	45.8% <66.7%> (+0.1%)	⬆️
CPAC/registration/registration.py	45.3% <80.6%> (+1.1%)	⬆️

... and 1 file with indirect coverage changes

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[shnizzedy]

I'm not sure where this is happening, but from the smoke tests it looks like something here makes sbref unavailable to coregistration in most of the other preconfigs? (this issue isn't happening in develop)

[birajstha]

I'm not sure where this is happening, but from the smoke tests it looks like something here makes sbref unavailable to coregistration in most of the other preconfigs? (this issue isn't happening in develop)

Thanks for review @shnizzedy , Will look into it.

[birajstha]

@shnizzedy , an error on my end. I had added a if statement that was blocking the other nodeblocks to be added to the workflow.
Should be resolved now.

[shnizzedy]

@shnizzedy , an error on my end. I had added a if statement that was blocking the other nodeblocks to be added to the workflow. Should be resolved now.

Thanks!

Rerunning the smoke tests,

• abcd-options still takes forever (I think that's out-of-scope for this PR and shouldn't block)
• ccs-options crashes OOM (#2277 should fix that)
• rodent fails with

  KeyError: "When trying to connect node block 'qc_xcp' to workflow 'cpac_pipeline_analysis_sub-4007_ses-ofMaF' after node block 'vmhc': space-T1w_sbref"

  (#2277 might also fix that?)

the rest all pass!

I think this is good to go, and if the remaining problems aren't resolved in #2277, we can revisit those issues then.