In the future, please (1) start new topics rather than reopening older closed topics and (2) use the software support post template. You can see I have made these edits for you this time.
Are you talking about using precomputed Freesurfer derivatives, which is usually preferred over skipping not using freesurfer at all?
Thank you for the warm welcome, I will do the suggested next time I post.
Would you think it is nessesary to use freesurfer at all? It’s for a fmri project and the methodology is RSA.
For context I am in high school so I have limited knowledge, but I feel bad bothering my mentors. The envioronment is colab.
I ended up downloading freesurfer partially just to bypass the bug(mri_convert) - it is currently running I am not sure if it will work yet.
I would also appreciate any advice on this matter.
FreeSurfer is generally recommended for state-of-the-art, but given this is for a high school project, I suppose you’d be fine without it.
You will hit fewer bugs if you run via containers (e.g. Docker or Apptainer, if you are on a personal computer, you’d probably use apptainer). All the software you will need are bundled in the container. Executing with Docker - NiPreps
Enabling fmriprep allows for analyses on the brain surface instead of on voxels (if that’s important to you) and generally leads to better alignment bewteen the BOLD image and the anatomical image.