Outputed gradients don't appear to correspond to previously observed hippocampal gradients

[myousif9]

The current iteration of the pipeline runs to completion without any apparent problems though the gradients outputted don't appear to correspond to previously described hippocampal gradients.

First to show the averaged HCP reference gradients used for alignment:

G1:

G2:

Then to show the first two gradients from one subject from another dataset:

G1:

G2:

@jordandekraker if you had any thoughts or ideas why this might be happening?

[jordandekraker]

I believe this line https://github.com/myousif9/hippograd/blob/4b67049765260fe623b8397198704f82ae5553e3/hippograd/workflow/scripts/compute_gradients.py#L138 should take gm.aligned as its input. Incidentally, you should probably also save the lambda values

[jordandekraker]

Oh also i think in order for the alignment to proceed to need to specify a method (eg 'procrustes'). I'm not sure about that though, it might just default to procrustes