[Node] Error on "mriqc_wf.dwiMRIQC.ComputeIQMs.datasink"

Software Support
1

Hi all,
I’m new to learn fmriprep relevant knowledge, now i step to MRIQC and encountered some issues, please anyone experts in this community could help me?

:slight_smile:

Summary of what happened:

MRIQC version 24.1.0.dev0+g3fe90466.d20240417 was used to calculate the subject-level analysis, there were 56 subjects in total, and all subject folder generated the JOSN file, but almost half of them no figures and htmls generated. after checked the error, I found the wrong subjects were no info write into the sub-xxx_dwi.json file. I don’t know why this happened, cause all nifti file of each subjects are intact, include the json file. by the way i used heudoconv to convert all DICOM file into NIFTI format.

Command used (and if a helper script was used, a link to the helper script or the command generated):

I installed docker on windows, here is my code

$subids =  $(cat H:\MRI_data\sublist.txt)
foreach($indexs in 0..55)
{
$proc_subs = $subids[$indexs]
docker run -it --rm `
-v F:\attention_data\Nift:/data:ro `
-v F:\attention_data\MRIQC:/out `
nipreps/mriqc:latest /data /out participant --participant_label $proc_subs
}

Version:

MRIQC version 24.1.0.dev0+g3fe90466.d20240417

Environment (Docker, Singularity / Apptainer, custom installation):

docker on windows wsl2

Data formatted according to a validatable standard? Please provide the output of the validator:

passed the online validation

Relevant log outputs (up to 20 lines):

2024-04-25 03:15:14 | INFO     | niworkflows      | Generating visual report
2024-04-25 03:16:16 | WARNING  | nipype.interface | Estimated signal variation in the background was too small (MAD=0.0, sigma=11.2851)
2024-04-25 03:16:16 | WARNING  | nipype.interface | Estimated signal variation in the background was too small (MAD=0.0, sigma=11.2851)
2024-04-25 03:16:16 | WARNING  | nipype.interface | Estimated signal variation in the background was too small (MAD=0.0, sigma=11.2851)
2024-04-25 03:22:26 | WARNING  | nipype.workflow  | Storing result file without outputs
2024-04-25 03:22:26 | WARNING  | nipype.workflow  | [Node] Error on "mriqc_wf.dwiMRIQC.ComputeIQMs.datasink" (/tmp/work/mriqc_wf/dwiMRIQC/ComputeIQMs/_in_file_..data..sub-114..dwi..sub-114_dwi.nii.gz/datasink)

Screenshots / relevant information: Traceback:

    Traceback (most recent call last):
      File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/bids.py", line 188, in _run_interface
        json.dumps(
      File "/opt/conda/lib/python3.11/site-packages/simplejson/__init__.py", line 395, in dumps
        **kw).encode(obj)
              ^^^^^^^^^^^
      File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 300, in encode
        chunks = list(chunks)
                 ^^^^^^^^^^^^
      File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 714, in _iterencode
        for chunk in _iterencode_dict(o, _current_indent_level):
      File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 645, in _iterencode_dict
        yield _floatstr(value)
              ^^^^^^^^^^^^^^^^
      File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 351, in floatstr
        raise ValueError(
    ValueError: Out of range float values are not JSON compliant: nan