Recon-all-clinical command in Freesurfer Docker

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1

Hi FreeSurfer experts,

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?

Appreciate your help,

2

Hi @wbano and welcome to neurostars!

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.

Best,
Steven

3

Hi Steven

Thanks for the prompt reply. Does the docker command would then look like this? Please excuse my limited knowledge of docker commands.

docker run -ti --rm -v /Applications/freesurfer/license.txt:/opt/freesurfer/license.txt freesurfer/freesurfer:7.4.1/bin/recon-all-clinical.sh -s Sub09 -i /Users/finnbrainpons/Desktop/2023-05-Desktop/2022-Wajiha/freesurfer_test/sub-09/ses-01/anat/sub-09_ses-01_run-01_T2w.nii

Regards
Wajiha

4

Hi @wbano,

No, it may look like this

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.

Best,
Steven

5

Hi Steven

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.

Regards

6

Hi @wbano,

Sorry I made a mistake above (I mainly use Singularity). --rm is not a part of docker exec, and docker run should be the correct command to use. I have edited my above post to reflect the changes.

Best,
Steven

7

Thanks a lot for your help.

8

As I mentioned above, do not use docker exec, use the edited version of the code I posted.

Also,

This is not correct the way you put it. You can either just put 3 there, or keep just $NTHREADS there if you define it before the docker run command (e.g., with NTHREADS=3).

Best,
Steven