Docker directory

mindboggle

#1

Hi,

We wanted to re-run mindboggle with the following specification: --no_moments --no_spectra

However, we realised that the normal mindboggle command doesn’t seem to be working, even thought it
was fine for a us a few months ago, using the same environment.

HOST=/c/Users/sb09/dockershare2
DOCK=/home/jovyan/work
IMAGE=$DOCK/T1.nii.gz
ID=ab12

running the command given on the mindboggle website:

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

we get the following error:

INFO: /root/matlab/startup.m does not exist … creating
/neurodocker/startup.sh: line 5: /home/jovyan/work/T1.nii.gz: No such file or directory

…eventhough T1.nii.gz is in the directory

Has something changed that isn’t specified in the documentation?

Thanks
Sophia


#2

Can you try:

docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle --entrypoint=bash $IMAGE

From there, verify that /home/jovyan/work/T1.nii.gz exists.

If it does, cat /neurodocker/startup.sh. It may be that the calling convention changed.