Docker run freesurfer no results

Software Support
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1

Summary of what happened:

I run freesurfer in Docker Desktop on Windows10, command:
image
But no results to output, I don’t know whether command is wrong or not

Command used (and if a helper script was used, a link to the helper script or the command generated):

docker run -i --rm -v D:\Results\license.txt:/opt/freesurfer/license.txt -v D:\Results:/data --env SUBJECTS_DIR=/data/freesurfer fmriprep:v1 parallel -j 0 recon-all -s Sub05 -i /data/rawmridata/Sub05/anat/Sub05_Sag_3D_T1-MPRAGE_20190308153919_3_Crop_1.nii -all

Version:

Environment (Docker, Singularity, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:

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2

Hi @conquerorlzq,

It would be good to know what error you are getting, but I think I see what is wrong with your command.

Your command should follow the basic format:

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

Here are the changes I would make:

I believe in FreeSurfer, the license is expected at /usr/local/freesurfer/.license

I don’t think this is a valid container. How about using the official container at freesurfer/freesurfer:7.3.2 (most recent stable version)?

I do not know what these flags are doing before your recon-all command.

In summary:

docker exec -i --rm -v D:\Results\license.txt:/usr/local/freesurfer/.license \ 
-v D:\Results:/data --env SUBJECTS_DIR=/data/freesurfer \ 
freesurfer/freesurfer:7.3.2 recon-all -s Sub05 \ 
-i /data/rawmridata/Sub05/anat/Sub05_Sag_3D_T1-MPRAGE_20190308153919_3_Crop_1.nii \ 
-all

Best,
Steven