Maintenance of Applications of DL in neuroimaging module

[soupeeli]

Module to maintain

Website: https://school-brainhack.github.io/modules/dl_for_neuroimaging/

Code: https://github.com/school-brainhack/school-brainhack.github.io/tree/main/content/en/modules/DL_for_neuroimaging

The tasks through the module maintenance

• creating an issue for the module of interest(s) in the Brainhack School Repo and assigning yourself to it,
• going through the module and assignment,
• editing the issue with the necessary changes found out,
• making the necessary corrections in the modules in a discussion with others,
• make the PR with the corrections, and integrate the reviews.
  

Works to be done:

• In the website https://school-brainhack.github.io/modules/dl_for_neuroimaging/ , Exercise section, the second line: "This part is independent from the video above.", might be better changed to "the video below"
• In https://main-educational.github.io/brain_encoding_decoding/intro.html , at the end of "Brain decoding vs. encoding" section (above Setup section), the figure for "Brain decoding with GCN" is broken, and the link for "Brain encoding using ridge regression" should be corrected from https://main-educational.github.io/brain_encoding_decoding/gcn_decoding.html to -> https://main-educational.github.io/brain_encoding_decoding/encoding.html ; Also, the link for "Brain decoding with SVM" and "Brain decoding with MLP" are broken as well, should be corrected to -> https://main-educational.github.io/brain_encoding_decoding/svm_decoding.html and -> https://main-educational.github.io/brain_encoding_decoding/mlp_decoding.html , respectively.
• When setting up the virtual env using https://github.com/main-educational/brain_encoding_decoding/blob/main/binder/requirements.txt , it failed to install torch-scatter==2.0.8 (with bug info saying no module named torch). The reason might be that the torch==1.13.0 installed before this was overwritten into other torch versions when installing other libraries before the torch-scatter. If now we reinstall the torch==1.13.10 and run pip install torch-scatter==2.0.8, it solves the problem. So I would suggest checking the dependencies between libraries in that requirement.txt file, and maybe re-order them to avoid this issue.

[htwangtw]

Thanks for checking on these issues!
Would you mind doing a PR to update the dependencies?