mriqc: OSError: No command "mri_robust_template" found with MRIQC v 23.1.0
What happened?
I have tried the new version (23.0.1) of MRIQC but I encountered the following error:
OSError: No command "mri_robust_template" found on host skylake103.cluster. Please check that the corresponding package is installed.
What command did you use?
singularity run --cleanenv -B /scratch/jsein/BIDS:/work \
/scratch/jsein/my_images/mriqc-23.1.0.simg /work/$study \
/work/$study/derivatives/mriqc23p1 participant group --participant_label $subjs --n_procs 12 \
-w /work/temp_data23p1_${study} --fd_thres 0.5 --verbose-reports
What version of the software are you running?
23.0.1
How are you running this software?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
230614-17:21:04,693 cli IMPORTANT:
Running MRIQC version 23.1.0:
* BIDS dataset path: /work/NEMO.
* Output folder: /work/NEMO/derivatives/mriqc23.
* Analysis levels: ['participant', 'group'].
230614-17:21:15,968 cli WARNING:
IMPORTANT: Anonymized quality metrics (IQMs) will be submitted to MRIQC's metrics repository. Submission of IQMs can be disabled using the ``--no-sub`` argument. Please visit https://mriqc.readthedocs.io/en/latest/dsa.html to revise MRIQC's Data Sharing Agreement.
230614-17:22:22,436 nipype.workflow WARNING:
Storing result file without outputs
230614-17:22:22,438 nipype.workflow WARNING:
[Node] Error on "mriqc_wf.dwiMRIQC.dwi_reference_wf.epi_merge" (/work/temp_data23p1_NEMO/mriqc_wf/dwiMRIQC/dwi_reference_wf/_in_file_..work..NEMO..sub-pilote1..dwi..sub-pilote1_dir-AP_dwi.nii.gz/epi_merge)
230614-17:22:24,269 nipype.workflow ERROR:
Node epi_merge.a0 failed to run on host skylake103.cluster.
230614-17:22:24,270 nipype.workflow ERROR:
Saving crash info to /work/NEMO/derivatives/mriqc23/logs/crash-20230614-172224-jsein-epi_merge.a0-da3ec52e-c696-4c3f-895a-9740bf13016c.txt
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 60, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.9/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 epi_merge.
Cmdline:
echo Only one time point!
Stdout:
Stderr:
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
raise IOError(
OSError: No command "mri_robust_template" found on host skylake103.cluster. Please check that the corresponding package is installed.
Additional information / screenshots
MRIQC v23.0.0 worked well on this dataset. It seems here that it is the dwi workflow that fails. The dwi
folder contains two dwi series, with the same b values, one acquired with phase encoding direction in A>P and the other in P>A, with 3 shells (b=300, b=1000 and b2000) with 7 additional b0.
About this issue
- Original URL
- State: closed
- Created a year ago
- Reactions: 2
- Comments: 21 (15 by maintainers)
@oesteban, any updates on this? I have a large dataset that would definitely benefit from the DWI QC workflow if it can get up and running.
I second this error.
This will be fixed in the next release.
I ran the same command on T1w, T2w and bold images only (with the
-m T1w T2w bold
argument) and everything went fine. It seems that the bug only affects the dwi workflow.