MRG, ENH: Create a tutorial for how to find intracranial electrode contacts from a CT and an MR image by alexrockhill · Pull Request #9484 · mne-tools/mne-python

alexrockhill · 2021-06-16T17:54:26Z

Addresses part of #9155.

This is a tutorial for how to:

Align a CT to an MR using Dipy
Find the electrode contacts using a GUI (another PR for the GUI but it's the img_pipe one)
Warp the electrode contacts to fsaverage using Dipy

This prepares you to start the working with SEEG and working with ECoG tutorials which require you to already have electrode positions in MNI space before starting but don't explain how you find them.

larsoner · 2021-06-16T18:07:56Z

@alexrockhill feel free to ping me when I should look

alexrockhill · 2021-06-16T18:15:32Z

Just a WIP so far but probably tomorrow

alexrockhill · 2021-06-17T17:37:39Z

Ok @larsoner, if you have time to review once the artifact renders, this is a good first draft.

It does look like the SDR does a better job with the morph than the Talairach:

SDR (this is actually for cvs_avg35_inMNI152 not fsaverage)

Talairach

alexrockhill · 2021-06-17T17:40:44Z

The references won't work until #9480 merges though....

alexrockhill · 2021-06-17T17:48:30Z

Uh oh I think the SDR takes longer than 10 minutes... not sure how to fix that

alexrockhill · 2021-06-17T20:48:55Z

I'm not sure what the latest error was but maybe rebasing will take care of it. I still think it's probably related to execution time. I'll look in the SDR tests for source space to see if there's a way to do things faster...

generating gallery for auto_tutorials/clinical... [ 25%] 10_ieeg_localize.py
  19.0 s : 456.8 MB   
ERROR:mprof:Program resulted with a non-zero exit code: -9
make: *** [Makefile:65: html_dev-pattern-memory] Error 247

alexrockhill · 2021-06-18T02:32:21Z

Ok so still failing with the weird error. I'm going to try profiling the code but the SDR function and maybe the affine registrations too might need to be added to misc data so that they can just be loaded instead of computed.

alexrockhill · 2021-06-18T17:36:29Z

I'm not sure what the latest error was but maybe rebasing will take care of it. I still think it's probably related to execution time. I'll look in the SDR tests for source space to see if there's a way to do things faster...
generating gallery for auto_tutorials/clinical... [ 25%] 10_ieeg_localize.py
  19.0 s : 456.8 MB   
ERROR:mprof:Program resulted with a non-zero exit code: -9
make: *** [Makefile:65: html_dev-pattern-memory] Error 247

I have no idea what this error means, if anyone had a chance to give it a look that would be appreciated.

alexrockhill · 2021-06-18T17:41:37Z

program.prof.zip

Ok, I know it's not rendering but it does run locally and it would be great to get a review of the content @larsoner if you have a minute. Here is the cProfile output as well that can be visualized, it looks like the affine registration just takes a long time but it does run in just over ten minutes.

alexrockhill · 2021-06-19T03:52:23Z

Hmmm so there's an issue that the affine_registration from Dipy doesn't work to align the CT and MR... I have used the nipy histogram registration but it isn't a dependency... Looking into reimplementing

larsoner · 2021-06-19T12:44:57Z

Is it expected to work? If so, might be worth opening an issue on dipy, they might know a workaround

We could add another dependency if histogram registration is expected to work on most cases

alexrockhill · 2021-06-19T14:21:42Z

Is it expected to work? If so, might be worth opening an issue on dipy, they might know a workaround

We could add another dependency if histogram registration is expected to work on most cases

I don't think so, I don't think Dipy has any reason to use or have tested anything using CT images.

The Nipy histogram registration is written in cython so that would be a bit harder to reimplement, but I could give it a try and see how slow it is in pure python...

alexrockhill · 2021-06-19T16:55:11Z

So this last version has all the parts working but there is some confusion converting between nibabel and nipy image objects that is not ideal. This adds a nipy dependency but I'm not sure how else to register the CT to the MR.

I think I'm going to start on the GUI next week and we can continue to iterate on this.

update version fixed the transform, the issue was units added myself as author, probably good for answering questions since I collected the data fix detrend issue so many ways to format notes had to move note finally fixed the note and fixed in the other ieeg example too more specific extra space fix note in ECoG working on ieeg contact localization tutorial

…for later

alexrockhill · 2021-06-23T23:34:17Z

Ok, I think that addressed all your comments @larsoner, I think the changes from your commit caused a few tests to fail though...

alexrockhill · 2021-06-23T23:34:57Z

Once mne-tools/mne-misc-data#6 merges, we should be good to go.

larsoner

Great progress! I think working on this example is useful for seeing what actually needs to be done to make this work, thanks for sticking with it. The align_volumes seems like the simplest solution I can think of, but if you see problems with it maybe we should have a quick chat tomorrow.

Also if you are sick of iterating on this and want to move onto GUI I can try implementing my suggested changes locally. I can also fix the tests I broke if it would help.

tutorials/clinical/10_ieeg_localize.py

alexrockhill · 2021-06-24T00:36:13Z

Also if you are sick of iterating on this and want to move onto GUI I can try implementing my suggested changes locally. I can also fix the tests I broke if it would help.

If you wouldn't mind fixing the tests you broke, I'm not exactly sure what you were doing there. You're welcome to make some changes if you'd like, I stopped working on it today.

larsoner · 2021-06-24T00:37:16Z

I won't get to it until tomorrow morning EDT but I'll push something then after pulling your latest changes

alexrockhill · 2021-06-24T00:48:49Z

I won't get to it until tomorrow morning EDT but I'll push something then after pulling your latest changes

Thanks for all the help! Sounds good, I think what needs to happen is that the tests need to be fixed and if you want to refactor the SDR morph you could do that but I might save it for a followup PR as it's going to affect the other SDR tests.

mne/surface.py

…ed it

… tut

alexrockhill · 2021-06-24T02:45:12Z

Ok, I'm happy to keep iterating if you have a chance to look at it tomorrow @larsoner but this looks like a viable tutorial to me

larsoner · 2021-06-24T15:00:12Z

Thanks @alexrockhill !

alexrockhill · 2021-06-24T17:12:16Z

requirements_doc.txt

 sphinx_copybutton
 https://github.com/mne-tools/mne-bids/archive/main.zip
 pyxdf
+nipy


We probably don't need this

alexrockhill force-pushed the tut branch from 1596d1c to f911411 Compare June 16, 2021 17:57

alexrockhill force-pushed the tut branch from 72ea2b4 to f44d68c Compare June 17, 2021 20:47

alexrockhill added 13 commits June 19, 2021 13:52

save changes to finish doc PR

cf2d2ba

added recon-all

d26bba8

draft of align and warp tutorial

b86964b

try adding dependency, probably remove later, fix typo

f06d10d

scaling is off by 1000, but I think also one transform

c837c79

okay working version, ready for review once it renders

075804f

try turning down the level iters

d93172e

hey not so bad to implement vtk marching cubes and hopefully helpful …

268d9d4

…for later

lowering the level iters doesn't work

f8aa8e3

working but nipy/nibabel confused looking version

8e5a3f0

add requires vtk

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didn't save properly

db24efb

alexrockhill force-pushed the tut branch from b24aba5 to db24efb Compare June 19, 2021 20:53

update latest

0f18739

alexrockhill added 4 commits June 23, 2021 15:23

that's better needed more factors

080c50e

alignment into code block

acf5420

okay really final version

8855822

flake

1107ac8

larsoner reviewed Jun 24, 2021

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remove acpc, rename CT

af4a052

FIX: Revert bad logic

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larsoner reviewed Jun 24, 2021

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alexrockhill added 4 commits June 23, 2021 18:16

thought about removing recon but you need it for the brain so explain…

bbf4df4

…ed it

changed to scipy label, but super slow

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revert

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Merge branch 'tut' of https://github.com/alexrockhill/mne-python into…

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… tut

larsoner added 5 commits June 24, 2021 09:18

DOC: Dep [skip azp] [skip github]

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FIX: Update [skip github] [skip actions]

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FIX: Update [skip github] [skip actions]

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FIX: Update [skip github] [skip actions]

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FIX: Update [skip github] [skip actions]

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larsoner mentioned this pull request Jun 24, 2021

Add color normalization parameter to plot_topomap #9468

Merged

larsoner changed the title ~~[WIP, ENH] Create a tutorial for how to find intracranial electrode contacts from a CT and an MR image~~ MRG, ENH: Create a tutorial for how to find intracranial electrode contacts from a CT and an MR image Jun 24, 2021

larsoner merged commit 44f5ecb into mne-tools:main Jun 24, 2021

alexrockhill commented Jun 24, 2021

View reviewed changes

This was referenced Jun 24, 2021

[MRG, MAINT] Remove Nipy Dependency, Note to explain voxel_neighbors #9504

Merged

[ENH] Add "roi" feature to mne.viz.Brain #9520

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