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kylemath / pyoptical

Imagent optical imaging interface to MNE loading
MIT License
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Coregister and plot channel coordinates on the scalp #16

Open kuziekj opened 4 years ago

kuziekj commented 4 years ago

We need to figure out how to import channel coordinates to info.dig and plot all channels on the scalp. Some resources that may help:

https://mne.tools/dev/auto_tutorials/source-modeling/plot_source_alignment.html#plot-source-alignment https://mne.tools/dev/auto_examples/visualization/plot_montage.html https://mne.tools/dev/auto_examples/visualization/plot_eeg_on_scalp.html https://mne.tools/dev/auto_tutorials/intro/plot_40_sensor_locations.html#sphx-glr-auto-tutorials-intro-plot-40-sensor-locations-py https://mne.tools/dev/generated/mne.channels.make_dig_montage.html?highlight=make_dig_montage#mne.channels.make_dig_montage

kylemath commented 4 years ago

there seems to be a function load load .elp files directly into info structures: https://mne.tools/dev/overview/implementation.html#dig-formats

kuziekj commented 4 years ago

yeah I tried it but it seemed like it wasn't loading the file properly.

when I tried to load an elp file with 411 channels, the function only returned info for around 22 of those channels, starting at channel 30 or so, and some of the coordinates it returned weren't correct for those channels.

Maybe I just didn't pass the right arguments to the function....I'm also assuming an elp is an elp and the equipment shouldn't change the format of the elp file (function seems to want an ISOtrak file).

anyway I can play around with the function again. we can also manually pass channel labels/coords to make a montage with this function:

https://mne.tools/dev/generated/mne.channels.make_dig_montage.html?highlight=make_dig_montage#mne.channels.make_dig_montage

kylemath commented 4 years ago

yes I think using the in build functions to make the .loc and .dig is a good idea since it will force them into the correct format, check, etc.

On Mon, Apr 27, 2020 at 8:25 AM kuziekj notifications@github.com wrote:

yeah I tried it but it seemed like it wasn't loading the file properly.

when I tried to load an elp file with 411 channels, the function only returned info for around 22 of those channels, starting at channel 30 or so, and some of the coordinates it returned weren't correct for those channels.

Maybe I just didn't pass the right arguments to the function....I'm also assuming an elp is an elp and the equipment shouldn't change the format of the elp file (function seems to want an ISOtrak file).

anyway I can play around with the function again. we can also manually pass channel labels/coords to make a montage with this function:

https://mne.tools/dev/generated/mne.channels.make_dig_montage.html?highlight=make_dig_montage#mne.channels.make_dig_montage

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-- Kyle E. Mathewson, Ph.D. Assistant Professor - Department of Psychology, Faculty of Science Director - Attention Perception and Performance Lab Affiliate - Neuroscience and Mental Health Institute, Faculty of Medicine and Dentistry University of Alberta P455 - Biological Sciences Building 11455 Saskatchewan Dr. Edmonton, Alberta, Canada, T6G 2E9 Phone: 1-780-492-2662 Email: kyle.mathewson@ualberta.ca Web: www.kylemathewson.com

kuziekj commented 4 years ago

coords are transformed

need to get info.dig to plot

kylemath commented 4 years ago

relevant discussion in: https://github.com/mne-tools/mne-python/pull/6856