Error in selecting --output-spaces MNIPediatric:cohort-5:res-2

[hfxcarl]

What happened?

Running latest 23.2.0 fmriprep on QTAB OpenNeuro dataset and specifying --output-spaces MNIPediatric:cohort-5:res-2.

What command did you use?

singularity run --cleanenv \
    -B /OpenData/QTAB/QTAB/BIDS_raw:/data:ro \
    -B /OpenData/QTAB/QTAB/BIDS_raw_DB:/pybids_db:ro \
    -B /OpenData/QTAB/QTAB/derivatives/fmriprep:/derivs \
    -B /scratch/QTAB/QTAB/fmriprep:/work \
    -B /opt/templateflow:/templateflow \
    /opt/SingularityImgs/fmriprep-23.2.0.sif \
    /data \
    /derivs \
    participant \
    --participant_label 0005 \
    -w /work \
    --bids-database-dir /pybids_db \
    --nprocs 8 \
    --omp-nthreads 8 \
    --mem 16  -v \
    --no-sub \
    --resource-monitor \
    --skip_bids_validation \
    --notrack \
    --output-spaces MNIPediatricAsym:res-2:cohort-5 MNI152NLin2009cAsym:res-2 \
    --cifti-output

What version of fMRIPrep are you running?

23.2.0

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

## log:
240301-15:16:51,788 nipype.workflow IMPORTANT:
         Running fMRIPrep version 23.2.0

         License NOTICE ##################################################
         fMRIPrep 23.2.0
         Copyright 2023 The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
240301-15:17:24,665 nipype.workflow IMPORTANT:
         Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['0005'].
           * Run identifier: 20240301-151603_c1ba3932-78fe-429c-b836-29d64fbe294b.
           * Output spaces: MNIPediatricAsym:cohort-5:res-2 MNI152NLin2009cAsym:res-2.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /derivs/sourcedata/freesurfer.
240301-15:17:48,878 nipype.workflow INFO:
         ANAT Stage 1: Adding template workflow
240301-15:17:50,199 nipype.workflow INFO:
         ANAT Stage 2: Preparing brain extraction workflow
240301-15:17:50,262 nipype.workflow INFO:
         ANAT Stage 3: Preparing segmentation workflow
240301-15:17:50,265 nipype.workflow INFO:
         ANAT Stage 4: Preparing normalization workflow for ['MNIPediatricAsym:cohort-5', 'MNI152NLin2009cAsym', 'MNI152NLin6Asym']
240301-15:17:50,285 nipype.workflow INFO:
         ANAT Stage 5: Preparing surface reconstruction workflow
240301-15:17:50,301 nipype.workflow INFO:
         ANAT Stage 6: Preparing mask refinement workflow
240301-15:17:50,303 nipype.workflow INFO:
         ANAT Stage 7: Creating T2w template
240301-15:17:50,309 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
240301-15:17:50,325 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
240301-15:17:50,331 nipype.workflow INFO:
         ANAT Stage 8a: Creating cortical ribbon mask
240301-15:17:50,334 nipype.workflow INFO:
         ANAT Stage 9: Creating fsLR registration sphere
240301-15:17:50,337 nipype.workflow INFO:
         ANAT Stage 10: Creating MSM-Sulc registration sphere
240301-15:19:21,170 nipype.workflow INFO:
         No single-band-reference found for sub-0005_ses-01_task-rest_dir-AP_bold.nii.gz.
240301-15:19:21,231 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
240301-15:19:21,236 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
240301-15:19:21,242 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
240301-15:19:21,272 nipype.workflow IMPORTANT:
         BOLD series will be slice-timing corrected to an offset of 0.416s.
…
…
…
240301-21:04:26,746 nipype.workflow INFO:
         [MultiProc] Running 0 tasks, and 32 jobs ready. Free memory (GB): 0.02/0.02, Free processors: 8/8.
240301-21:04:26,869 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.select_MNI6" in "/work/fmriprep_23_2_wf/sub_0005_wf/select_MNI6".
240301-21:04:26,871 nipype.workflow INFO:
         [Node] Executing "select_MNI6" <niworkflows.interfaces.utility.KeySelect>
240301-21:04:27,135 nipype.workflow INFO:
         [Node] Finished "select_MNI6", elapsed time 0.000601s.
240301-21:04:27,136 nipype.workflow INFO:
         [Job 453] Completed (fmriprep_23_2_wf.sub_0005_wf.select_MNI6).
240301-21:04:27,259 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" in "/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2/select_xfm".
240301-21:04:27,261 nipype.workflow INFO:
         [Node] Executing "select_xfm" <niworkflows.interfaces.utility.KeySelect>
240301-21:04:27,526 nipype.workflow INFO:
         [Node] Finished "select_xfm", elapsed time 0.000435s.
240301-21:04:27,526 nipype.workflow WARNING:
         Storing result file without outputs
240301-21:04:27,526 nipype.workflow WARNING:
         [Node] Error on "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" (/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2/select_xfm)
240301-21:04:27,526 nipype.workflow ERROR:
         Node select_xfm.a0 failed to run on host worf.
240301-21:04:27,527 nipype.workflow ERROR:
         Saving crash info to /derivs/sub-0005/log/20240301-151603_c1ba3932-78fe-429c-b836-29d64fbe294b/crash-20240301-210427-uher-select_xfm.a0-68ceb294-2750-489c-acc8-5ab045166844.txt
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/lib/python3.10/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 select_xfm.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
            outputs = self.aggregate_outputs(runtime)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 429, in aggregate_outputs
            predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/utility.py", line 217, in _list_outputs
            index = self.inputs.keys.index(self.inputs.key)
        ValueError: 'MNIPediatricAsym:cohort-5' is not in list


240301-21:04:27,546 nipype.workflow INFO:
         [Job 454] Completed (fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm).
240301-21:04:27,672 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" in "/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.res2/select_xfm".
240301-21:04:27,674 nipype.workflow INFO:
         [Node] Executing "select_xfm" <niworkflows.interfaces.utility.KeySelect>
240301-21:04:27,941 nipype.workflow INFO:
         [Node] Finished "select_xfm", elapsed time 0.000498s.
240301-21:04:27,942 nipype.workflow INFO:
         [Job 455] Completed (fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm).

Additional information / screenshots

I think there might be a naming issue including "cohort-5" twice? (_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2):

Specific line from above log:
240301-21:04:27,259 nipype.workflow INFO:
[Node] Setting-up "fmriprep_23_2_wf.sub_0005_wf.template_iterator_wf.select_xfm" in "/work/fmriprep_23_2_wf/sub_0005_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-5.cohort5.res2/select_xfm".

[mgxd]

This was fixed in nipreps/smriprep#416, hoping to get a new release out with the fix this week.

BTW, I believe the MNIPediatricAsym:res-2:cohort-5 in your command should be MNIPediatricAsym:cohort-5:res-2, as cohort is parsed before resolution.

[effigies]

We should probably not be sensitive to the order of the modifiers.

[WangYunHong98]

Hi all @effigies @mgxd

I have the same issue ValueError: ‘MNIPediatricAsym:cohort-1’ is not in list in fmriprep 23.2.1.


And this is the argument --output-spaces MNIPediatricAsym:res-1:cohort-1 used in my script.

Has this issue been solved or can I use other versions released before fmriprep 23.2.1.

Best,
Yunhong