FastSurfer: Problem running with multiple subjects

Software Support
,
1

Summary of what happened:

I am running FastSufer for multiple subjects, but I don’t get it whether the problem is with the ‘–entrypoint’ flag or docker.

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

sudo docker run --gpus all \
-v /home/user1nrx/software_research/my_fastsurfer_analysis/DATA:/data \
-v /home/user1nrx/software_research/my_fastsurfer_analysis/OUTPUT:/output \
-v /home/user1nrx/software_research/my_fastsurfer_analysis/freesurfer_license:/fs_license \
--entrypoint "/fastsurfer/brun_fastsurfer.sh" \
 --rm \
--user $(id -u):$(id -g) \
deepmi/fastsurfer:latest \
--fs_license /fs_license/license.txt \
--sd /output \
--subject_list /data/subjects_list.txt \
--parallel \
--3T \
/fastsurfer/brun_fastsurfer.sh \
--fs_license /fs_license/license.txt -\
-sd /output --subject_list \
/data/subjects_list.txt \
--parallel \ 
--3T

Version:

Environment:

sudo docker pull deepmi/fastsurfer:latest

Docker

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

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

INFO: run_fastsurfer not explicitly specified, using $FASTSURFER_HOME/run_fastsurfer.sh.
ERROR: Flag unrecognized.

Screenshots / relevant information:

2

Hi @FARAH_NAZ,

In a lot of software pipeline containers, you do not have to set an entrypoint, as the default will be to run the workflow (in this case, FastSurfer).

Best,
Steven

3

The problem was solved after changing the paths for each subject in the subjects_list.txt from “/home/user1nrx/software_research/my_fastsurfer_analysis/DATA” to “/data”. Apparently the path i was providing was outside the container.