Download the required softwares (freesurfer
, ANTs
and anaconda
).
bash download.sh
Since we only need mri_synthseg
and mri_synthstrip
commands from freesurfer
, we can filter out all the other binaries and models. Run the following as root:
bash reduce-freesurfer.sh
Finally, build the Docker container:
docker build -t lemuelpuglisi/turboprep .
This is a cpu
version of turboprep. Hopefully, a gpu version will come next. If you need to preprocess a lot of data, I strongly suggest to run the local version of turboprep (see the main README).