README `Slicer`

Description. This repo primarily contains scripts to perform whole-brain deterministic tractography on single-shell data, using 3D Slicer and whitematteranalysis software, and the O'Donnell Research Group (ORG) atlas. Specifically, the directory contents are as follows:

• 01_scripts. These 10 scripts take in the lab's preprocessed DWI data, and run all subsequent steps ultimately required for tractography. The scripts should, more or less, be run sequentially: most rely on outputs made in prior scripts.
• 02_visualization. These 3 scripts pull together images generated by whitematteranalysis quality control scripts. The files can be knitted and posted to rpubs.com for easy group review.
• 03_analysis. The script in /notebooks provides summary tables and visualizations of missing data across participants and tracts.

Note. Example data is not included here, butcan be found in the whitematteranalysis tutorial.

Requirements. The scripts require (i) input data to be in BIDS format, and (ii) access to the ORG atlas. Software dependencies are indicated at the top of each script.

Important links:
ORG atlas
whitematteranalysis wiki
whitematteranalysis tutorial