Compute only metrics (no corrections) over fmriprep freesurfer output with MRIQC

Hi experts,

I know that this is not how MRIQC is supposed to be used, but I have a question for you.

I used fmriprep to preprocess my data, and I am going to use SPM and pyMVPA for, respectively, GLM and MVPA. However, it turned out that I got some problems in the preprocessed data so I am going to delete my fmriprep folder (but keep the freesurfer one) and start the preprocessing again.

Since I wasn’t aware (my bad) of MRIQC and its usage, I didn’t run any quality metric on my raw images. so now my question is: is there any reasonable way I can run MRIQC on the raw images OR (even better) on the freesurfer/fmriprep folder to get quality metrics without needing to restart from scratch? The freesurfer surface extraction is quite time-consuming, so it would be great if I would be able to keep the work done so far.


I think the quality metrics from MRIQC will not tell you much out of the box. You’ll need to explore them if you want to really extract any information from them.

However, I think using MRIQC’s reports to visualize and assess the data is a bit of a must.

MRIQC is meant to be quick & dirty, so it does not depend on FreeSurfer (nor its results).

I think you’d be interested in reading this protocol (also preprint).

Awesome, thanks for helping out!