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rmldj / hcp-utils

Utilities to use HCP and HCP-like data with nilearn and other Python tools
MIT License
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citing use of package #5

Closed amsinha9 closed 2 years ago

amsinha9 commented 3 years ago

Do you have a preferred citation we should use in publications if we display results of brain figures using hcp-utils?

rmldj commented 3 years ago

Thanks! I am really glad that it's useful. Please cite the github URL of the package. Btw. I would be happy if at some stage you could e-mail me your paper..

amsinha9 commented 3 years ago

Yes, once it has been accepted, we will share the paper. Do you know if there is a way to generate half of the 3D brain image to plot the subcortical parcels? We are trying to edit the source code in hcp_utils.py to only show the left hemisphere and the corresponding left parcels. We are wondering if we could edit the function load_surfaces and do something similar to below:

for hemisphere, hemisphere_name in [('L', 'left')]:
     elif count==1:
                #meshes[variant] = meshes[variant+'_left']
rmldj commented 3 years ago

You mean subcortical? Then there is no way using hcp_utils as it uses nilearn's surface plot which plots only cortical surfaces (as I discussed in the other issue).

I now remember that once I made some 3d plot with subcortical structures using matplotlib 3d but that was rather ugly and slow. I do not know if I can locate the script...