Summary of what happened:
A continuation of a prior issue. Dataset is now BIDS valid and is confirmed by the BIDS validator. Working on a single subject with just a T1w and single functional run. MRIQC will run for around an hour and 30 min, then will spit out the netstat and 3dinfo error.
I searched for netstat and 3dinfo in the sif: singularity exec np_mriqc_latest.sif which netstat 3dinfo /opt/afni/3dinfo I see 3dinfo but not netstat.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run -e $sifloc --participant-label $subj --n_procs 4 --omp-nthreads 4 --mem_gb 16 --no-sub --ica --fft-spikes-detector -vvv -w $workdir $indir $outdir participant
Version:
MRIQC v23.1.0rc0
Environment (Docker, Singularity, custom installation):
singularity build np_mriqc_latest.sif docker://nipreps/mriqc:latest
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes.
bids-validator@1.8.0
1: [WARN] Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing. (code: 38 - INCONSISTENT_SUBJECTS)
./sub-SPIN001/func/sub-SPIN001_task-rest_bold.json
Evidence: Subject: sub-SPIN001; Missing file: sub-SPIN001_task-rest_bold.json
./sub-SPIN001/func/sub-SPIN001_task-rest_bold.nii.gz
Evidence: Subject: sub-SPIN001; Missing file: sub-SPIN001_task-rest_bold.nii.gz
./sub-SPIN004/anat/sub-SPIN004_FLAIR.json
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_FLAIR.json
./sub-SPIN004/anat/sub-SPIN004_FLAIR.nii.gz
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_FLAIR.nii.gz
./sub-SPIN004/anat/sub-SPIN004_T2w.json
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_T2w.json
./sub-SPIN004/anat/sub-SPIN004_T2w.nii.gz
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_T2w.nii.gz
./sub-SPIN004/fmap/sub-SPIN004_acq-rest_dir-AP_run-01_epi.json
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_acq-rest_dir-AP_run-01_epi.json
./sub-SPIN004/fmap/sub-SPIN004_acq-rest_dir-AP_run-01_epi.nii.gz
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_acq-rest_dir-AP_run-01_epi.nii.gz
./sub-SPIN004/fmap/sub-SPIN004_acq-rest_dir-AP_run-02_epi.json
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_acq-rest_dir-AP_run-02_epi.json
./sub-SPIN004/fmap/sub-SPIN004_acq-rest_dir-AP_run-02_epi.nii.gz
Evidence: Subject: sub-SPIN004; Missing file: sub-SPIN004_acq-rest_dir-AP_run-02_epi.nii.gz
... and 24 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=INCONSISTENT_SUBJECTS for existing conversations about this issue.
2: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
27 Files, 1.1GB rest MRI
3 - Subjects
1 - Session
Relevant log outputs (up to 20 lines):
Traceback (most recent call last):
File "/opt/conda/bin/mriqc", line 8, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/mriqc/cli/run.py", line 168, in main
mriqc_wf.run(**_plugin)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 184, in run
self._clean_queue(jobid, graph, result=result)
File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 256, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: 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 gcor.
Cmdline:
@compute_gcor -mask /data/ncl-mb13/mriqc_work/mriqc_wf/funcMRIQC/ComputeIQMs/_in_file_..data..ncl-mb13..SPIN_TEST..sub-SPIN004..func..sub-SPIN004_task-rest_bold.nii.gz/gcor/sub-SPIN004_task-rest_bold_valid_volreg_tstat_mask.nii.gz -input /data/ncl-mb13/mriqc_work/mriqc_wf/funcMRIQC/ComputeIQMs/_in_file_..data..ncl-mb13..SPIN_TEST..sub-SPIN004..func..sub-SPIN004_task-rest_bold.nii.gz/gcor/sub-SPIN004_task-rest_bold_valid_volreg.nii.gz
Stdout:
** failed to get view of -input /data/ncl-mb13/mriqc_work/mriqc_wf/funcMRIQC/ComputeIQMs/_in_file_..data..ncl-mb13..SPIN_TEST..sub-SPIN004..func..sub-SPIN004_task-rest_bold.nii.gz/gcor/sub-SPIN004_task-rest_bold_valid_volreg.nii.gz, check command
Stderr:
/bin/netstat: Command not found.
3dinfo: Command not found.
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.9/site-packages/mriqc/interfaces/transitional.py", line 89, in _run_interface
gcor_line = [
IndexError: list index out of range
Screenshots / relevant information:
Side question - I’m still experimenting with a very minimal dataset (just a T1w and single functional run). Does MRIQC extend to work on AP and PA images?