Jordan DeKraker

removed valueError for nonzero eigenvalues

4

I was rtying to run this for hippocampal surfaces with no masked data (i.e. no medial wall) and received an error on this line. I believe it is an unneeded...

Add links and documentation for some of the extended projects being worked on by me (eg. matlab code for visualization of DG), Brad (matlab code for laplace-constrained DWI modelling), Uzair...

long staging

1

Lately i've been submitting hippunfold jobs from within a `regularSubmit -j LongSkinny` job because building the DAG and staging takes so long. Possible bottlenecks: - If my understanding is correct,...

simplified outputs by concatenating label-hipp/dentate

2

This is just an idea, and I'd like to hear feedback @akhanf @royhaast @myousif9 @Bradley-Karat I was thinking it might be nice to concatenate label-`hipp` and `dentate` output files (they...

wetrun testing

2

Currently, I have pulled some opensource data: https://osf.io/k2nme/ and Doc here: https://github.com/khanlab/hippunfold/pull/303 TODO: - ideally, we should make all of these wetrun data into a snakemake workflow and automate -...

This should help clarify the terminology - we will simply replace all instances of `atlas` with `parc`. This is a breaking change. We will wait until the BIDS spec defines...

AD trained model

5

work by @Bradley-Karat

auto-afids for optimization

2

[autoafids](https://github.com/afids/autoafids) could be a nice way to speed up cropping to bounding box! Maybe also in a contrast-agnostic way. Edit: Link to the correct autoafids repository.

script reusability outside snakemake

2

Currently all python scripts are interacted with using `snakemake.inputs.x` or `snakemake.outputs.y`. This makes them very annoying to use outside of a snakemake workflow, e.g., for one-time use or applying code...

adding `--modality neonateT1w` can simplify the workflow to already apply `--modality T1w` `--template dHCP` `--force-nnunet-model neonateT1w_v2` @mahmoud1yaser and/or @Dhananjhay