This repository contains the skeleton for the CIMH neuroimaging workshop.
This repository was created using the G0RELLA template
Open an issue on this repository and someone will try and get back to you as soon as possible!
Neuroimaging Workshop
Home Page: https://johanneswiesner.github.io/workshop_cimh/
License: BSD 3-Clause "New" or "Revised" License
This repository contains the skeleton for the CIMH neuroimaging workshop.
This repository was created using the G0RELLA template
Open an issue on this repository and someone will try and get back to you as soon as possible!
if [[ "$OSTYPE" == "linux-gnu"* ]]; then
singularity run -B /zi-flstorage/group_csp/analyses/johannes.wiesner/projects/hcp_project/code/:/home/neuro/workdir \
-B /zi-flstorage/group_csp/open_access_datasets/humanconnectome/raw_data/:/data \
-B /zi-flstorage/group_csp/open_access_datasets/humanconnectome/derivatives/:/output \
/csp-tools/singularity_images/csp_neurodocker/csp.sif jupyter-lab --notebook-dir=/home/neuro/workdir
elif [[ "$OSTYPE" == "msys" ]]; then
winpty docker run -it --rm -v /C:/Users/Johannes.Wiesner/Documents/projects/hcp_project/code/:/home/neuro/workdir \
-v /C:/Users/Johannes.Wiesner/Documents/projects/hcp_project/data/humanconnectome/raw_data/:/data \
-v /C:/Users/Johannes.Wiesner/Documents/projects/hcp_project/data/humanconnectome/derivatives/:/output \
-p 8888:8888 johanneswiesner/csp:1.0.0 jupyter lab
fi
Don't use python here, we had problems with a Windows machine that couldn't execute this code in Git Bash because Python wasn't installed.
Workshop won't have an introduction to datalad so I guess we don't need users to install WSL+datalad?
Run root-branch from neurodocker to generate right folder structure. Combine this with #5
Windows users should be able to use Git Bash to download course material. For this, we have to tweak the bash script:
Add ANTS + FSL so we can run a minimal-preprocessing pipeline for the anatomical workflow
VSCode + Docker installation is nice, but if we only stick to jupyter-notebooks a docker image with jupyter-lab included would be sufficient?
Use this script https://github.com/JohannesWiesner/workshop_cimh/blob/master/run_docker.sh so users already use the right folder paths for their analysis
Instead of adding a /data folder to the github repository, one should be able to use
https://nilearn.github.io/dev/modules/generated/nilearn.datasets.fetch_spm_auditory.html
to download the auditory spm dataset. The problem is that we need to find a way to retrieve this dataset without nilearn as we can't rely on people having python + nilearn installed before the workshop
This offers other users templates for these questionnaires (and also makes it possible to use other providers than redcap).
Currently, we use both
from nilearn.datasets import fetch_oasis_vbm and fetch_spm_auditor from nilearn to download data (functional and anatomical).
1.) That takes time during the workshop (would be nice if participants could do this beforehand)
2.) We cannot be sure that people end up with firewall-issues in the workshop (smarter to tell participants to download before workshop so we can debug stuff in case something goes wrong).
Download of this image can take a while so people should do the download together with the data download in download_courses.sh
Make sure that spm.SPMCommand().version
works. All the necessary stuff should be already set in the Dockerfile (avoid confusing users): https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.spm.base.html
As long as there are no other workshops beside nipype + docker, we don't need a separate python installation but can just use a docker image.
https://wiki.ubuntuusers.de/ACL/
acl has to be installed first (add to apt-get at the beginning of Dockerfile)
Then use setfacl
to set full permission (read+write+execute) on all the folders (/home/csp/data, /home/csp/output, etc.)
https://wiki.ubuntuusers.de/ACL/#Setzen-und-Loeschen-von-ACLs
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