Summary of what happened:
Error using MNIPediatricAsym:cohort-3 template with fMRIprep – ValueError: ‘MNIPediatricAsym:cohort-3’ is not in list. Exception raised while executing Node select_xfm.
I have had success using --output-spaces MNIPediatricAsym:res-1:cohort-3 with previous versions of fMRIprep (23.1.0, 20.2.3).
Command used (and if a helper script was used, a link to the helper script or the command generated):
# Set directories
singularity_dir="/storage/group/klk37/default/sw"
bids_root_dir="/storage/group/klk37/default/R01_Marketing/bids"
# Run the job itself
unset PYTHONPATH
singularity run --cleanenv $singularity_dir/fmriprep-23.2.0.simg \
$bids_root_dir/raw_data $bids_root_dir/derivatives/preprocessed/fmriprep_v2320 \
participant \
--participant_label 002 \
--verbose \
--output-spaces MNIPediatricAsym:res-1:cohort-3 \
--fs-license-file $FS_LICENSE \
--work-dir $bids_root_dir/code/fmriprep/sub-002/work_v2320
Version:
23.2.0
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.14.0
(node:1054779) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
^[[33m1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)^[[39m
^[[36m Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.^[[39m
^[[33m2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)^[[39m
^[[36m Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.^[[39m
^[[33m3: [WARN] The Name field of dataset_description.json is present but empty of visible characters. (code: 115 - EMPTY_DATASET_NAME)^[[39m
^[[36m Please visit https://neurostars.org/search?q=EMPTY_DATASET_NAME for existing conversations about this issue.^[[39m
^[[34m^[[4mSummary:^[[24m^[[39m ^[[34m^[[4mAvailable Tasks:^[[24m^[[39m ^[[34m^[[4mAvailable Modalities:^[[39m^[[24m
809 Files, 6.34GB foodview MRI
26 - Subjects sst
1 - Session
Relevant log outputs (up to 20 lines):
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
