BIDS Formatting for MRIQC Output

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1

Hi everyone,
I am using the following Docker command to run MRIQC:

docker run -it --rm -v /mnt/c/path/to/BIDS/folder:/data:ro" -v /mnt/c/path/to/mriqc/folder:/out nipreps/mriqc:latest /data /out participant --participant_label 01

The HTML reports are currently stored in the mriqc folder instead of sub-01. Should these reports be moved to the sub-01 folder to comply with BIDS formatting, or is there a more appropriate location within the mriqc directory? Below is the current directory structure for reference.

BIDS/
└── sub-01/
    ├── ses-one/
    │   └── anat/
    │       ├── sub-01_ses-one_run-01_T1w.nii.gz
    │       └── sub-01_ses-one_run-01_T1w.json
    └── ses-two/
        └── anat/
            ├── sub-01_ses-two_run-01_T1w.nii.gz
            └── sub-01_ses-two_run-01_T1w.json
derivatives/
└── mriqc/
    ├── sub-01/
    │   ├── ses-one/
    │   │   └── anat/
    │   ├── ses-two/
    │   │   └── anat/
    │   └── figures/
    ├── sub-01_ses-one_run-01_T1w.html
    └── sub-01_ses-two_run-01_T1w.html

Additionally, I have a similar question regarding the FreeSurfer output for structural generated by fMRIPrep. Would it be better to create a separate post for that?

Edit: fixed the filenames to reflect that there is more than one run.

Many thanks in advance!

2

The base of the mriqc directory is fine for the HTMLs. I’m not up to date with the specifics of the BIDS derivatives, or where HTMLs fall into that framework, but the outputs of BIDS apps will generally follow whatever BIDS standard is available for that data type.

I’m less familiar with FreeSurfer, but would assume the same general principle applies.