Skip to content

Conversation

effigies
Copy link
Member

While attempting to reproduce a bug report, I ran across a crash. Fieldmaps are always in RAS, while the BOLD references and masks are in the space of the original BOLD. In the case of ds000221, that's LSP. The reportlet assumes all input images are in the same space, and so can fail if the field-of-view is not a cube (and would be bad otherwise).

I was unable to reproduce the reported bug, but it's possible it was confused for this. For searchability's sake, the error was:

2024-10-21 12:21:37,963 [CRITICAL] fMRIPrep failed: Traceback (most recent call last):
  File "/home/chris/mambaforge/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/chris/mambaforge/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/chris/mambaforge/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/chris/mambaforge/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node sdecreg_report.

Traceback:
        Traceback (most recent call last):
          File "/home/chris/mambaforge/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 398, in run
            runtime = self._post_run_hook(runtime)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/chris/mambaforge/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/mixins/reporting.py", line 50, in _post_run_hook
            self._generate_report()
          File "/home/chris/Projects/nipreps/sdcflows/sdcflows/interfaces/reportlets.py", line 103, in _generate_report
            abs(np.percentile(fmapdata[maskdata], 99.8)),
                              ~~~~~~~~^^^^^^^^^^
        IndexError: boolean index did not match indexed array along dimension 1; dimension is 88 but corresponding boolean dimension is 64

I'm calling this a bug-fix because the workflow change occurred in a non-critical path (reports) and there is no risk of pollution from an existing working directory.

Copy link

codecov bot commented Oct 24, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.78%. Comparing base (1248b63) to head (c4014f2).
Report is 8 commits behind head on maint/24.1.x.

Additional details and impacted files
@@               Coverage Diff                @@
##           maint/24.1.x    #3387      +/-   ##
================================================
- Coverage         71.79%   71.78%   -0.02%     
================================================
  Files                57       57              
  Lines              4255     4256       +1     
  Branches            459      458       -1     
================================================
  Hits               3055     3055              
  Misses             1086     1086              
- Partials            114      115       +1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Copy link
Collaborator

@mgxd mgxd left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm - opened nipreps/sdcflows#467 to either catch or address this in the reportlet

@effigies effigies merged commit 0218f4f into nipreps:maint/24.1.x Oct 24, 2024
14 of 16 checks passed
@effigies effigies deleted the fix/sdcreg_report branch October 24, 2024 17:06
@effigies effigies added this to the 25.0.0 milestone Mar 19, 2025
effigies added a commit that referenced this pull request Mar 25, 2025
25.0.0 (March 25, 2025)

New feature release in the 25.0.x series.

This release substantially improves support for pre-computed derivatives.
Previous releases would miss some derivatives and rerun the computations.
Note that derivatives from previous versions will be accepted,
so it should not be necessary to recompute derivatives from previous versions.
The recommended command line is::

    fmriprep BIDS_DIR OUT_DIR participant --derivatives fmriprep=PRECOMP_DIR

Note that multiple derivatives can be specified, for example::

    fmriprep BIDS_DIR OUT_DIR participant \
      anat=PRECOMPUTED_ANATOMICAL_DIR \
      func=PRECOMPUTED_FUNCTIONAL_DIR

When the same file is found in multiple derivatives, the last one found takes precedence.

Additionally, `--force-*` flags have been consolidated into a single
`--force` flag that can take multiple, space-separated arguments.

Structural processing changes
-----------------------------
We now output white, pial and midthickness fsLR meshes on the subject surface.
Look for `sub-<subject>_hemi-<L|R>_space-fsLR_*_<surf>.surf.gii` files.

Brain extraction has been modified slightly to more closely match the
`antsBrainExtraction.sh` workflow distributed by ANTs.
The impact should be minimal, but in rare cases this fixes a crash.

Fieldmap processing changes
---------------------------
SyN-SDC fieldmap filtering is now single-level, following the improvements
for gradient-echo fieldmaps in 24.1.

Jacobian-weighting during fieldmap unwarping is now on by default *only*
for PEPolar fieldmaps.
To enable for other fieldmap types, use `--force fieldmap-jacobian`.

All merged pull requests
------------------------

* FIX: Detect and apply precomputed fieldmaps (#3439)
* FIX: Calculate bold mask and dummy scans in transform-only runs (#3428)
* FIX: Use consistent skull-stripping pre- and post- SDC (#3415)
* FIX: Use removeprefix instead of lstrip or ternary operator (#3409)
* FIX: Listify sessions when generating reports (#3408)
* FIX: Ensure fieldmap is resampled correctly in report (#3387)
* FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
* FIX: Repair and test query for precalculated baseline/boldref files (#3370)
* FIX: Repair search for precomputed transforms (#3369)
* ENH: Enable Jacobians only for PEPOLAR by default, allow forcing (#3443)
* ENH: Create `--force` flag that accepts a list, replacing individual `--force-*` flags (#3442)
* ENH: Output fsLR meshes on subject surfaces (#3411)
* ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution (#3393)
* ENH: Update FSL packages for reported bug fixes (#3374)
* RF: Calculate RMSD from motion transforms (#3427)
* RF: Reconstruct motion confounds from minimal derivatives (#3424)
* RF: Replace deprecated pkgutil.find_loader (#3384)
* RF: Upgrade nitransforms and remove workarounds (#3378)
* DOC: Fix xfm extension in the outputs docs (#3435)
* DOC: Mention fMRIPost-AROMA in parser documentation (#3356)
* MNT: Remove CLI flags with expired deprecation periods (#3445)
* MNT: Update pinned environment (#3440)
* MNT: Bump pins, update RTD config (#3425)
* MNT: Declare linux/amd64 platform during Docker build (#3422)
* MNT: Bump astral-sh/setup-uv from 4 to 5 (#3417)
* MNT: Test support for Python 3.13 (#3416)
* MNT: Install Workbench CLI via conda (#3410)
* MNT: Update minimum dependencies, test with tox-uv (#3412)
* MNT: Install c3d through conda (#3382)
* CI: Fetch tags and 200 commits to support describe (#3381)
* CI: Build docker images in GHA, store cache inline and push to GHCR (#3380)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants