Diffusion tool box that combines Vistasoft, MRtrix3, LiFE and AFQ to produce white matter connectomes. It requires the toolboxes mentioned before to be installed. The pipeline is orgnized as below.
A great place to start exploring this pipeline is the script "fat/preprocessing/scripts/fatPreprocmrTrix3WrapperLocal.m", which includes the entire pipeline from raw dti data to connetomes. The pipeline is organized as follows:
- Prepare fat data and directory structure
- Preprocess the data using mrTrix3
- The preprocessing flips our bvecs. We don't want that, so we copy our original bvecs from the raw folder. We also fix the nifti header.
- Initiate a dt.mat data structure
- Set up tractography for mrtrix 3
- Create a better wm mask with FreeSurfer
- Create connectomes with MRtrix3
- Optional: Run LiFE to optimize the connectome
- Optional: Run AFQ to classify the connectome
- Optional: Clean Connectome with AFQ
In addition to this preprocessing pipeline, what include an assortment of analysis and plotting function that might come in handy.