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kingjr / ecoggui

Ecog GUI is a Python module to localize intracranial electrodes from MRI.
BSD 2-Clause "Simplified" License
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TODO #1

Open kingjr opened 8 years ago

kingjr commented 8 years ago
choldgraf commented 8 years ago

Small update on 3D plotting because I figured it might be relevance here. I've been making progress on the 3D plotting with the plotly folks. I have a PR that gets the trisurf function to go from ~15 seconds to around ~2 seconds (not including the OpenGL call).

Makes some fairly pretty brains :) maybe it can be useful for plotting brains after the co-registration as a sanity check?

image

I'm also going to take another look into pycortex. That group isn't super good about updating their documentation etc, but I'm gonna try to sift through it and figure out what functionality it gives.

choldgraf commented 8 years ago

ps sorry for taking so long on the response here...it's been a crazy 3 months (long story)

choldgraf commented 8 years ago

And w/r/t switching between CT / MRI / pre/post MRI / etc, are you thinking of implementing a class to handle multiple volumes that belong to the same brain? That could be a way to relatively quickly go from one data type to another. Might be a good way to deal with co-registration as well, if we want to go down that path.

kingjr commented 8 years ago

Wow, that's the most beautiful 3D brain I've ever seen! Do you have a link/gist/PR?

Nibabel has merged the 3D viewer, so I need to rebase this rep. It's still low priority for me since there's someone who does the elec location manually, I don't get the motivation to spend time on this.

choldgraf commented 8 years ago

Haha, I know right? Sadly that's an MNI brain, so our recon brains would probably be way crappier :P

I don't have code to reproduce yet because we actually uncovered a bug in the javascript plotly uses. I hear a fix is coming tomorrow so I'll post something once it's working!

I didn't realize a 3D viewer was coming to nibabel. Is that 3D as in 3D surface, or 3D as in showing images from 3 axes?

kingjr commented 8 years ago

Oh so this isn't python?

3 axes only. It very close to what is used on this rep.

On Tuesday, 24 May 2016, Chris Holdgraf notifications@github.com wrote:

Haha, I know right? Sadly that's an MNI brain, so our recon brains would probably be way crappier :P

I don't have code to reproduce yet because we actually uncovered a bug in the javascript plotly uses. I hear a fix is coming tomorrow so I'll post something once it's working!

I didn't realize a 3D viewer was coming to nibabel. Is that 3D as in 3D surface, or 3D as in showing images from 3 axes?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/kingjr/ecoggui/issues/1#issuecomment-221458245

choldgraf commented 8 years ago

The call to trisurf is python, but plotly converts it to javascript and plots using OpenGL (or WebGL, can't remember which). The syntax is basically the same as the mayavi trisurf function.

Sounds good re: nibabel, better to offload as much as we can onto another package and build cool stuff on top of that :)

On Tue, May 24, 2016 at 7:51 PM, Jean-Rémi KING notifications@github.com wrote:

Oh so this isn't python?

3 axes only. It very close to what is used on this rep.

On Tuesday, 24 May 2016, Chris Holdgraf notifications@github.com wrote:

Haha, I know right? Sadly that's an MNI brain, so our recon brains would probably be way crappier :P

I don't have code to reproduce yet because we actually uncovered a bug in the javascript plotly uses. I hear a fix is coming tomorrow so I'll post something once it's working!

I didn't realize a 3D viewer was coming to nibabel. Is that 3D as in 3D surface, or 3D as in showing images from 3 axes?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/kingjr/ecoggui/issues/1#issuecomment-221458245

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/kingjr/ecoggui/issues/1#issuecomment-221460107