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Running micapipe_cleanup with Docker
Hello everyone,
I am trying to run micapipe_cleanup using a linux machine with docker. However I keep getting the error that the repository does not exist.
I have been using the following command:
docker run -it micalab/micapipe:latest micapipe_cleanup (arguments...)
The following command also did not work for me:
docker run -it micalab/micapipe:latest /opt/micapipe/functions/micapipe_cleanup (arguments...)
Could anyone help me with constructing a proper Docker command? Thank you in advance!
I'd love to see an example of a proper docker command for the cleanup as well. I've had no success guessing how this should be done.
Hi @jinseo0904 & @dkp,
sorry for the late reply. Could you maybe share the respective full commands that you tried to run?
Cheers, Peer
@PeerHerholz and @jinseo0904 here's what I tried:
docker run -ti --rm \
-v ${PWD}/inputs:/bids_dataset:ro \
-v ${PWD}/outputs:/output_directory \
-v ${PWD}/working:/tmp \
-v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
micalab/micapipe:latest \
-bids /bids_dataset \
-out /output_directory \
-sub 219 -ses itbs \
/opt/micapipe/functions/micapipe_cleanup -proc_rsfmri
Hi @dkp,
thx for the information. Hm, not entirely sure tbh. Could you please try the following:
At first, start the container, entering the bash
docker run -ti --rm \
-v ${PWD}/inputs:/bids_dataset:ro \
-v ${PWD}/outputs:/output_directory \
-v ${PWD}/working:/tmp \
-v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
--entrypoint /bin/bash \
micalab/micapipe:latest
and then from within the bash
run
micapipe_cleanup \
-bids /bids_dataset \
-out /output_directory \
-sub 219 -ses itbs \
-proc_rsfmri
Cheers, Peer
Sorry to take so long to get back to you.
The first command correctly put me inside the container...but there, it seems the micapipe_cleanup script cannot be found:
root@3c84af9079b8:/home/mica# micapipe_cleanup -bids /bids_dataset -out /output_directory -sub 219 -ses itbs -proc_rsfmri
bash: micapipe_cleanup: command not found
root@3c84af9079b8:/home/mica# which micapipe_cleanup
root@3c84af9079b8:/home/mica# micapipe_cleanup
bash: micapipe_cleanup: command not found
Hi there,
sorry for the late reply. Oh, entering via bash
might not correctly source
paths
, etc. . Could you please try to run
bash /neurodocker/startup.sh
after you entered the container
via the shell
and before you try to run micapipe_cleanup
?
Cheers, Peer
@PeerHerholz Thank you for the suggestion, unfortunately running the startup script does not seem to find micapipe_cleanup. I'm happy to try other suggestions and I appreciate your time.
-Dianne
root@6269bc0c63be:/home/mica# bash /neurodocker/startup.sh
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /opt/freesurfer-6.0.0
FSFAST_HOME /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects
MNI_DIR /opt/freesurfer-6.0.0/mni
FSL_DIR /opt/fsl-6.0.0
root@6269bc0c63be:/home/mica#
root@6269bc0c63be:/home/mica# micapipe_cleanup -bids /bids_dataset -out /output_directory -sub 219 -ses itbs -proc_rsfmri
bash: micapipe_cleanup: command not found
root@6269bc0c63be:/home/mica# micapipe_cleanup
bash: micapipe_cleanup: command not found
root@6269bc0c63be:/home/mica#
Hi, we took this suggestion for our next release v0.1.3
which is being built ATM. With the new release micapipe_cleanup
can be call within the main script micapipe
to avoid this issues. Please stay tuned for the new container release