I successfully ran mriqc for each participant with the --participant_label option.
Now I am trying to run just the group analysis with the following:
singularity run --cleanenv -B /home -B /scratch -B /project -B /project/6019291/shared/Proj/derivatives -B $HOME:/home/kgeier /home/kgeier/mriqc-0.15.1.simg /home/kgeier/projects/rrg-brad/shared/Proj /home/kgeier/projects/rrg-brad/shared/Proj/derivatives/mriqc/groupOut group
However I get the following error:
Running MRIQC version 0.15.1:
* BIDS dataset path: /project/6019291/shared/Proj.
* Output folder: /project/6019291/shared/Proj/derivatives/mriqc/groupOut.
* Analysis levels: group.
Traceback (most recent call last):
File “/usr/local/miniconda/bin/mriqc”, line 10, in
File “/usr/local/miniconda/lib/python3.7/site-packages/mriqc/bin/mriqc_run.py”, line 295, in main
raise Exception(“No data found. No group level reports were generated.”)
Exception: No data found. No group level reports were generated.
The “No data found” part surprises me as from what I understand, it should find the output of participant level mriqc files automatically based on it being in BIDS format. Currently the output is in Proj/derivatives/mriqc/sub-X/sub-X_T1w.html (e.g with T1 structural but I also have functional scans).
Would anybody please be able to help me with why the data is not being found? Is there some issue with the BIDS format? Does it have to do with running mriqc through a singularity and binding the wrong directories?
Any help on this matter would be greatly appreciated
Thanks so much,