DWMRI preprocessing pipeline with topup and eddy
- Install FSL
- Download repos and (optional) example data:
git clone https://github.com/justinblaber/system_utils.git
git clone https://github.com/justinblaber/nifti_utils.git
git clone https://github.com/justinblaber/dwmri_visualizer.git
git clone https://github.com/justinblaber/topup_eddy_preprocess.git
# Optionally download example data
wget https://justinblaber.org/downloads/github/topup_eddy_preprocess/scans.zip
unzip scans.zip
- In MATLAB:
>> addpath('system_utils');
>> addpath(genpath('nifti_utils'));
>> addpath(genpath('dwmri_visualizer'));
>> addpath('topup_eddy_preprocess');
If you've downloaded the example data, then edit the test script (only the fsl_path variable should have to be changed) and run it:
>> edit test_topup_eddy_preprocess
The output PDF should look like:
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