Summary of what happened:
Hello,
I am trying to use MRIQC on my FLAIR images. However, FLAIR as a modality does not exist. Since I know that FLAIR is a subcategory of T2w images, I changed each FLAIR suffix in the file names within my BIDS-conform data to T2w so that the command can recognize it as such. However, it still did not work unfortunately.
My question is: what should I do differently to what is stated right below?
Command used:
mriqc rawdata_tmp derivatives_tmp participant --participant-label 100000 -m T2w --no-sub --reports-only
Version:
MRIQC (v23.1.0)
Environment (Docker, Singularity / Apptainer, custom installation):
MRIQC is available as a module provided by my system’s administrator.
Data formatted according to a validatable standard? Please provide the output of the validator:
Already validated to be correct by BIDS Validator v1.14.6.
Relevant log outputs (up to 20 lines):
240709-14:07:58,827 nipype.workflow WARNING:
Storing result file without outputs
240709-14:07:58,828 nipype.workflow WARNING:
[Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (/data/one_sub_mriqc/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..data..one_sub_mriqc..rawdata_tmp..sub-100000..ses-01..anat..sub-100000_ses-01_acq-TRA_rec-DEFACED_T2w.nii.gz/measures)
240709-14:08:00,599 nipype.workflow ERROR:
Node measures.a0 failed to run on host zislrds0052.zi.local.
240709-14:08:00,600 nipype.workflow ERROR:
Saving crash info to /data/one_sub_mriqc/derivatives_tmp/logs/crash-20240709-140800-amrou.abas-measures.a0-9e3a3d33-776a-48ae-ba6e-8a15c1293cc5.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 measures.
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/mriqc/interfaces/anatomical.py", line 114, in _run_interface
raise RuntimeError(
RuntimeError: Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset.
Screenshots / relevant information:
Operating System: Ubuntu 22.04.3 LTS