fmriprep error "ValueError: 'MNIPediatricAsym:cohort-3' is not in list"

[emvdmeijden]

What happened?

I am trying to run fmriprep for preprocessing of resting state fmri data of a pediatric population with a mean age of 7.5. I would like to use the MNIPediatricAsym:cohort-3 template included in templateflow as output space for the spatial normalization of the T1w images, however I keep getting the error that this template is not in list (please see log output).

The $TEMPLATEFLOW_HOME environment is set to "/home/em23/.cache/templateflow" and includes the "tpl-MNIPediatricAsym" directory, which contains 6 cohort directories, license, scripts directory, and the template_description.json file. The cohort directories all contain nii.gz files for brain mask, CSF_probseg, GM_probseg, WM_probseg, PD, T1w, and T2w for both res-1 and res-2 (14 files per cohort).

I also ran fmriprep with the MNI152NLin2009cAsym template as the output space (this template is the default, so same command line used with --output-spaces flag omitted), which did not produce any errors.

Has anyone encountered this problem before while running fmriprep for a pediatric population? Many thanks in advance!

What command did you use?

fmriprep-docker home/em23/Desktop/fmriprep home/em23/Desktop/fmriprep_output participant --skip_bids_validation --participant-label 93 --fs-license-file usr/local/freesurfer/license.txt --ignore slicetiming --output-spaces MNIPediatricAsym:cohort-3

What version of the software are you running?

fMRIPrep v23.2.0

How are you running this software?

Docker

Is your data BIDS valid?

No

Are you reusing any previously computed results?

FreeSurfer

Please copy and paste any relevant log output.

Errors
Node Name: fmriprep_23_2_wf.sub_93_wf.template_iterator_wf.select_xfm

File: /out/sub-93/log/20240216-164851_5103920b-fdb1-4480-b5ae-d361c2f2d229/crash-20240216-191305-root-select_xfm.a0-65ff9fe2-92bf-4e29-acdc-f7f1c812bb60.txt
Working Directory: /tmp/work/fmriprep_23_2_wf/sub_93_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-3.cohort3.resnative/select_xfm
Inputs:

    anat2std_xfm: ['/out/sub-93/anat/sub-93_from-T1w_to-MNIPediatricAsym_mode-image_xfm.h5', '/out/sub-93/anat/sub-93_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5']
    key: MNIPediatricAsym:cohort-3
    keys: ['MNIPediatricAsym', 'MNI152NLin2009cAsym']

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-3' is not in list



Node Name: fmriprep_23_2_wf.sub_93_wf.anat_fit_wf.anat_reports_wf.template_iterator_wf.select_xfm

File: /out/sub-93/log/20240216-164851_5103920b-fdb1-4480-b5ae-d361c2f2d229/crash-20240216-191305-root-select_xfm.a0-c177ea7c-8cc6-468a-b53b-f3bc559eb63a.txt
Working Directory: /tmp/work/fmriprep_23_2_wf/sub_93_wf/anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-3.cohort3.resnative/select_xfm
Inputs:

    anat2std_xfm: ['/out/sub-93/anat/sub-93_from-T1w_to-MNIPediatricAsym_mode-image_xfm.h5', '/out/sub-93/anat/sub-93_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5']
    key: MNIPediatricAsym:cohort-3
    keys: ['MNIPediatricAsym', 'MNI152NLin2009cAsym']

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-3' is not in list

Additional information / screenshots

No response

[mgxd]

Thanks for the report, I was able to replicate the problem and am working on a fix.