I want to convert some .mgz file into .nii format using FreeSurfer, but I don’t have this software installed in my PC. I learned that the fMRIprep docker have packaged the FreeSurfer into its image. I am not an expert to Docker, so I want to ask if there is a way to run FreeSurfer from the fMRIprep docker?
Any suggestions would be appreciated.
You can use the fMRIPrep docker container, but FreeSurfer does have it’s own container as well (
docker pull freesurfer/freesurfer:7.3.2).
You can use something like:
docker exec [OPTIONS] CONTAINER COMMAND [ARG...]
singularity exec [OPTIONS] CONTAINER COMMAND [ARG...]
Thanks for your kind help. It is nice to know that FreeSurfer has it own container. I will have a try.