Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: Add white matter fiber tracking to sEEG tutorial #12555

Draft
wants to merge 15 commits into
base: main
Choose a base branch
from

Conversation

alexrockhill
Copy link
Contributor

This adds white matter tracking to the sEEG tutorial so that electrode contacts in white matter can be better interpreted.

@alexrockhill
Copy link
Contributor Author

Hey @skoudoro and @pjsjongsung, no rush, but when you have a spare few minutes, would you mind reviewing this? Specifically, there's a bit of an issue in the tutorial (tutorials/clinical/20_seeg.py) where the deterministic tracking yields very short, disconnected fibers. I'm wondering if you have any advice on parameters or methods to use to get more helpful fiber tracking. Right now I have it set to find fibers within 50 mm of an sEEG contact in white matter and there's a bunch of disconnected fibers but, ideally, it would be more specific, like 3 mm, and would show the pyramidal tract in this case (LPM 1 is a contact in white matter near left premotor cortex).

@skoudoro
Copy link

Hi @alexrockhill, I will look into it later this week. Can you share your peaks (the pam5 contains the peaks). I just want to make sure that they make sense. Not sure if your issue is due to the tractography or the peaks. Last time I encounter such an issue, it was due to the peaks so the reconstruction.

@alexrockhill
Copy link
Contributor Author

Here's the pam file: https://ohsuitg-my.sharepoint.com/:u:/r/personal/rockhill_ohsu_edu/Documents/pam_example/seeg_sample_pam.pam5?csf=1&web=1&e=u9ZkMk

Thanks for offering to review, really appreciate it.

@alexrockhill
Copy link
Contributor Author

@larsoner did you do the new release? I'm still getting MNE-misc-data version 0.27 with no diffusion images

@pjsjongsung
Copy link

pjsjongsung commented Apr 22, 2024

@alexrockhill it says user not in directory and I cannot access the link. Do you have another link you could share or change the permissions of that link?

Edit:
Just got the permission. Thanks!

@alexrockhill
Copy link
Contributor Author

I added your gmail and UI email. OHSU doesn't allow you to open up permissions unfortunately... I could have shared on Google Drive though... probably should have

@alexrockhill
Copy link
Contributor Author

@alexrockhill
Copy link
Contributor Author

@larsoner did you do the new release? I'm still getting MNE-misc-data version 0.27 with no diffusion images

Just pinging on this when you have a second @larsoner, thanks

@larsoner
Copy link
Member

I cut 0.28 a few weeks ago you need to update mne/datasets/config.py to tell it to use 0.28:

misc="0.27",

and the hash

hash="md5:e343d3a00cb49f8a2f719d14f4758afe",

But the version was wrong there (said 0.27 in the dataset itself) so I just cut a 0.29 so use that instead anyway

https://github.com/mne-tools/mne-misc-data/releases/tag/0.29

@alexrockhill
Copy link
Contributor Author

My bad, I forgot I had to do that, thanks!

@alexrockhill
Copy link
Contributor Author

@alexrockhill
Copy link
Contributor Author

Huh how do you ignore the vulture stuff? It is used... cc @larsoner

@larsoner
Copy link
Member

@drammock
Copy link
Member

Huh how do you ignore the vulture stuff? It is used...

to find this yourself next time: git grep vulture yields only 10 hits, the last of which is:

pyproject.toml:392:paths = ['mne', 'tools/vulture_allowlist.py']

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

5 participants