Run FreeSurfer from the fMRIprep docker

1

Hi everyone,

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.

Best,
Qunjun

2

Hi Qunjun,

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...]

or

singularity exec [OPTIONS] CONTAINER COMMAND [ARG...]

Best,
Steven

3

Hi Steven,

Thanks for your kind help. It is nice to know that FreeSurfer has it own container. I will have a try.

Best,
Qunjun