MRIQC Group Report

1

Hi All,

This might be a silly question. :slightly_smiling_face:
After I finish the mriqc with docker. I want to generate a group visual report.
from the doc, I should use mriqc.reports.group.gen_html to get…
But I don’t know how to use this function.
Any guidance?

Yun

2

Hi,

To generate the group report you need to run the group level analysis

mriqc bids-root/ output-folder/ group

where bids-root/ and output-folder/ should be the same as the ones you used for the participant level analysis. See http://mriqc.readthedocs.io/en/latest/running.html for more details.

3 Likes
3

Mmmm…I run it the mriqc for each subject separately within a loop…(>100 subjects).
Do I need to rerun ? If rerun, will it automatically skip finished procedures?

Thanks!

4

You do not need to rerun the loop you used for the participant stage. You only need to run the group level once now. It works because it will find the outputs of the participant stages in the output directory (the assumption being you used the same output folder for all participants when running the participant stage of mriqc).

This might be better explained in the Command line interface section of the BIDS Apps paper.