ABTIN

Absolute Tissue density from NODDI (ABTIN) is described here:

Brain Tissue Compartment Density Estimated Using Diffusion-Weighted MRI Yields Tissue Parameters Consistent With Histology Farshid Sepehrband, Kristi A. Clark, Jeremy F.P. Ullmann, Nyoman D. Kurniawan, Gayeshika Leanage, David C. Reutens, and Zhengyi Yang , Humman Brain Mapping, 2015. DOI: 10.1002/hbm.22872

Implementation (in MATLAB)

Download ABTIN's reposiotry. No additional download is required. The only dependency is MATLAB NIFTI toolbox, which is included in the repository.

1. NODDI

In order to obtain ABTIN's measures, first the NODDI model should be fitted to the diffusion-weighted MR data. To fit NODDI to your data, we suggest one of the following routines:

• NODDI MATLAB toolbox: follow the instruction here.
• AMICO: follow the instruction here.

2. Setup the path

• Add the path to this repostitory.

For example:

addpath(genpath('~/code/matlab/ABTIN-master/'))

3. Initialization

• Define the the path to the input folder of ABITN (folder contaning NODDI outputs)
• Define the the path to the output folder of ABITN

For example:

InputFolder='~/data/noddi/Sub-01';

OutputFolder = '~/data/abtin/Sub-01';

4. ABTIN

ABTIN(InputFolder,OutputFolder)

At this stage, ABTIN's outputs are stored in the output folder.

Script

"Demo.m includes the above steps."