search

nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
Other
143 stars 54 forks source link

Permissions issue: When I set host and dock I am unable to run mindboggle #139

Closed knutj closed 6 years ago

knutj commented 6 years ago

I have set HOST=/var/lib/docker and DOCK=/home/jovyan/work # path to HOST from Docker container IMAGE=$DOCK/T1.nii.gz # input image on HOST ID=arno # ID for brain image After I have copied T1.nii.gz into the container. When I use this command it crash with permmision problmes

docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle $IMAGE --id $ID

Buf if I use the command below I get mideboggle running.

docker run --rm -ti nipy/mindboggle $IMAGE --id $ID Create missing output directory /home/jovyan/work/mindboggle123_output Create missing working directory /home/jovyan/work/mindboggle123_output/working

binarybottle commented 6 years ago

Do you have permission to access /var/lib/docker? That seems to be the most likely problem, given that this is the only thing that deviates from the example command and $IMAGE is accessible with the second command.

knutj commented 6 years ago

I found a way to resolve my problem. I now use HOST=~/work and DOCK=/freesurfer. I did not have write permission to /var/lib/docker as this where I stored the container. Please add resolved.

knutj commented 6 years ago

please close.

binarybottle commented 6 years ago

Glad you were able to resolve the issue with a simple permission change. All the best!