ENH: Leverage T2w if available for BOLD -> anat coregistration #3208
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mgxd
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Jan 18, 2024
fmriprep/interfaces/patches.py
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| class MRICoregInputSpec(fs.registration.MRICoregInputSpec): | ||
| reference_file = File( | ||
| argstr="--ref %s", | ||
| desc="reference (target) file", | ||
| copyfile=False, | ||
| ) | ||
| subject_id = traits.Str( | ||
| argstr="--s %s", | ||
| position=1, | ||
| requires=["subjects_dir"], | ||
| desc="freesurfer subject ID (implies ``reference_mask == " | ||
| "aparc+aseg.mgz`` unless otherwise specified)", | ||
| ) | ||
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| class MRICoreg(fs.MRICoreg): | ||
| """ | ||
| Patched that allows setting both a reference file and the subjects dir. | ||
| """ | ||
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| input_spec = MRICoregInputSpec |
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this patch is needed to include the reference file + subject dir/id information in the outputted LTA
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #3208 +/- ##
==========================================
+ Coverage 72.03% 72.12% +0.09%
==========================================
Files 55 55
Lines 4101 4144 +43
==========================================
+ Hits 2954 2989 +35
- Misses 1147 1155 +8 ☔ View full report in Codecov by Sentry. |
effigies
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Jan 19, 2024
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
effigies
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Jan 25, 2024
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LGTM. Small comments at this point.
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
tsalo
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effigies
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Jun 17, 2024
24.0.0 (June 17, 2024) New feature release in the 24.0.x series. This release is an incremental improvement on 23.2.x, with some fixes for bugs discovered in the updated workflow. New features include separation of HTML reports by session for subjects with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability with less typical FreeSurfer directories, such as those generated by longitudinal FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow the recommendations of recent versions of BIDS. With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo and Wang Hao-Ting for their contributions! * FIX: Add "double" type to allowed DisplacementFieldTransform (#3287) * FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256) * FIX: Ensure proper templates are retrieved with sloppy (#3251) * FIX: Delete summary from functional report when separated by sessions (#3223) * FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215) * FIX: Re-enable anat fasttrack for dataset without t1w (#3202) * ENH: Use BIDSURI in init_ds_boldmask_wf (#3297) * ENH: Add templateflow to DatasetLinks (#3267) * ENH: Track proximal sources of functional GIFTIs (#3263) * ENH: Support named derivative paths (#3264) * ENH: Track Sources for standard-space outputs (#3262) * ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142) * ENH: Use BIDS URIs to track Sources in sidecars (#3255) * ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236) * ENH: Add metadata for motion parameters (#3245) * ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191) * ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208) * RF: Fix ITK warp conversion to nitransforms format (#3300) * RF: Load report assembler from nireports (#3177) * DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205) * TST: Update test to reflect new report generation behavior (#3210) * STY: Manual conversions to f-strings (#3241) * STY: Apply ruff/pyupgrade rule UP031 (#3280) * STY: Lint and style check full repository (#3221) * STY: Adopt ruff for linting and formatting (#3206) * MNT: Pin libitk 5.3 and note dependencies (#3298) * MNT: Upgrade ruff pre-commit, add fixing checks (#3283) * MNT: Complete transition from flake8/black to ruff (#3279) * MNT: Apply Repo-Review suggestions (#3194) * MNT: Verbatim copy of Apache license 2.0 (#3259) * MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234) * MNT: Drop copyright year, unused dunder fields (#3247) * MNT: Update environment pins (#3226) * MNT: Bump codecov/codecov-action from 3 to 4 (#3219) * DOCKER: Restore mincinfo binary (#3249) * CI: Move to new circle machine tags (#3248) * CI: Avoid ruff warning (#3244) * CI: Pass ruff tests (#3243)
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This PR adds a new parameter
use_t2wtoinit_bold_reg_wf, which enables/disables using a T2w reference as an intermediate for bbregister.As long as a T2w is found in the dataset, this option is enabled, as smriprep has already preprocessed and brought the T2w to T1w space.
This PR only changes the behavior of the
bbreg_wffork, the FSL workflow remains using the T1w reference.cc @madisoth as this was inspired based on some comparison work from him