Joshuazzzs
November 2, 2022, 11:53am
1
Hi!
pieper
November 2, 2022, 11:57pm
2
It looks like you need these instructions:
# Tutorial
This tutorial explains how to perform whole-brain tractography parcellation using the [whitematteranalysis (WMA)](https://github.com/SlicerDMRI/whitematteranalysis) software and the anatomically curated [O'Donnell Research Group (ORG)](http://dmri.slicer.org/atlases/) white matter atlas.
On this page, we provide step-by-step instructions to guide a user to run the entire tractography parcellation pipeline for **_an individual subject_**.
> We also provide a master shell script ```wm_apply_ORG_atlas_to_subject.sh``` (see documentation [here](https://github.com/SlicerDMRI/whitematteranalysis/blob/73a7948751f49d9fda8ec84fb5caeecaeeb92621/bin/wm_apply_ORG_atlas_to_subject.sh#L1-L40)) that enables running the whole pipeline in one command. However, we recommend the users to run through the following step-by-step tutorial first to get familiar with the whole fiber clustering pipeline.
> Note: ```wm_apply_ORG_atlas_to_subject.sh``` provides options to remove intermediate files to save disk space.
## 1. Software prerequisites
- Install [3D Slicer](https://download.slicer.org/)
> 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization.
- Install [SlicerDMRI](http://dmri.slicer.org/download/)
> SlicerDMRI is an open-source project to improve and extend diffusion magnetic resonance imaging software in 3D Slicer.
- Install [whitematteranalysis (WMA)](https://github.com/SlicerDMRI/whitematteranalysis#wma-installation)
> WMA is an open source software package for data-driven fiber clustering white matter parcellation.
## 2. Download tutorial data
- Download the tutorial data package ([WMA_tutorial_data.zip](https://www.dropbox.com/s/beju3c0g9jqw5uj/WMA_tutorial_data.zip?dl=0), ~2.5GB)
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