Francisco Dorr

Freesurfer 6.0.0-min missing files for recon-all -all

2

The default Freesurfer 6.0.0-min fails when running `recon-all -all` command (at least when `-parallel` and `-openmp` flags are on) . There are two missing files: `reconbatchjobs` and `mri_seg_diff` I added...

There is a big for loop that should be refactored to an outside function.

Current implementation doesn't store the bands for each constellation. It would be nice to have that info stored. Some ideas: - Store a simple metadata json at constellation level (easiest)...

I changed the matrix creation code to improve its performance by retrieving nonzero values from a sparse matrix. The _cell by cell_ iteration used before to check if cell was...

Segmentation classes description not available

1

I'm reading the code and the paper (highres3dnet_brain_parcellation) and I can't find what anatomical parcellation corresponds to each class. It would be great if there was a description for each...

- Fix error in get_bounded_footprint what was wrongly indexing by row instead of row_idx ``` Traceback (most recent call last): File "/home/fran/repos/Major-TOM/src/grid.py", line 318, in bbox = grid.get_bounded_footprint(point, buffer_ratio=0.1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^...