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?
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