I want to run recon-all-clinical to segment the T2w images I have where T1s are not available. I have pulled the Freesurfer 7.4.1 docker image but I cannot seem to find the command to use recon-all-clinical in that. Can anyone guide me regarding the docker command?
I had no problem finding recon-all-clinical.sh in my containerized version of 7.4.1 (Docker)
As you can see here (recon-all-clinical - Free Surfer Wiki), one in a Docker container might contain a bug anyway. So you can do download the version they link to there, and they in your Docker command, mount that version as /usr/local/freesurfer/bin/recon-all-clinical.sh, and then run it.
docker run -ti --rm \ # not docker run since we want to run a different command than the default
-v /Applications/freesurfer/license.txt:/opt/freesurfer/license.txt \ # mount your license
-v /PATH/TO/YOUR/recon-all-clinical.sh:/usr/local/freesurfer/bin/recon-all-clinical.sh \ # mount the fixed recon-all-clinical
-v /Users/finnbrainpons/Desktop/2023-05-Desktop/2022-Wajiha/freesurfer_test:/bids \ # mount your data directory
freesurfer/freesurfer:7.4.1 \ # the container
recon-all-clinical.sh \ # the command you want to run
bids/sub-09/ses-01/anat/sub-09_ses-01_run-01_T2w.nii \ # input data
sub-09 \ # subject ID
$NTHREADS \ # number of CPUs, defaults as 1 which is slow so you probably want to use more than that
/bids/derivatives/freesurfer # output directory
Please confirm you understand the code above and give it a try.
Thank you for sending me the command and bearing with me. I do get that docker exec is the command to run the script within the container but I am getting this error: first, it was ‘Unkown flag --rm’ and if I remove this then I get the error 'unknown shorthand flag: ‘v’ in -v.
Somehow it’s not recognising the mounting of the volumes. If you have any insights about it, that would be great.