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A. Installation

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Javier Gonzalez-Castillo edited this page Nov 3, 2021 · 2 revisions

In addition to several python libraries as described in the python environment .yaml file, this project also needs additional software and data that you will need to install first. We describe those next.

Required Software Packages

Required Brain Parcellations

Here, we use the 200 ROI version of the Scheffer Atlas (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal).

  1. Create a local folder for brain parcellations: (e.g., <DATA_DIR>/Atlases)

  2. Create a sub-folder for the 200 Schaefer Atlas named Schaefer2018_200Parcels_7Networks: (e.g., <DATA_DIR>/Atlases/Schaefer2018_200Parcels_7Networks)

  3. Copy the following files from their original location in CBIG repo (link above) to your local Schaefer Atlas folder:

  • stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_200Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
  • stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/freeview_lut/Schaefer2018_200Parcels_7Networks_order.txt
  • stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/fsleyes_lut/Schaefer2018_200Parcels_7Networks_order.lut
  • stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Centroid_coordinates/Schaefer2018_200Parcels_7Networks_order_FSLMNI152_2mm.Centroid_RAS.csv
  1. Write down the path to the local Schaefer Atlas folder, as you will need it in Step 1 of "How to run this code" below.

NOTE: By following this naming convention, it should be easy to use other atlases

NBS v1.2 Installation

  1. Create a folder where you will download the software
cd /data/SFIMJGC_HCP7T/
mkdir hcp7t_fv_env_extraSW
cd hcp7t_fv_env_extraSW

  1. Download NBS v1.2 from https://www.nitrc.org/projects/nbs and place it in the folder you just created

  2. Unzip the downloaded ZIP file

cd /data/SFIMJGC_HCP7T/hcp7t_fv_env_extraSW
unzip NBS1.2.zip
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