connectome-spatial-smoothing
Connectome Spatial Smoothing
Here, you may find the Python codes and sample scripts for Connectome Spatial Smoothing (CSS).
For more information you may check our article on Connectome Spatial Smoothing (CSS): concepts, methods and evaluation. All resources are provided as complementary to the following article:
Mansour, L. Sina, et al. “Connectome Spatial Smoothing (CSS): concepts, methods, and evaluation.” NeuroImage (2022): 118930.
The code used for this study is now released as a python package. If using the codes, please also cite the following:
The codes in this repository mainly perform the following tasks:
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Map high-resolution structural connectomes from tractography
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Map atlas-resolution structural connectomes from tractography
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Compute the CSS smoothing kernel with selected parameters
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Perform CSS on high-resolution connectomes
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Perform CSS directly on atlas connectomes
Installation
To use CSS functionality in your code, you can install the package with the following command:
pip install -U Connectome-Spatial-Smoothing
Then, you could simply use the package in your own code after importing:
from Connectome_Spatial_Smoothing import CSS as css
Usage notes
Verbosity:
By default CSS scripts print out a bunch of logs that may or may not be of interest to you. If you like to disable the logs, simply add the following script:
css._verbose = False
We have provided a short jupyter notebook showcasing all the functionalities described above. You may use the following link to open this notebook in an interactive google colab session:
Note: there has been a new release with added functionality that is explained in the following interactive notebook: