Minimal instructions:

On HUGIN:
* make sure you have gradient tables in a BXH file (e.g. from dicom2bxh)
* convert your DTI data to NRRD format (run bxh2nrrd)
* run /usr/local/packages/DTIPrep/DTIPrep (this will launch the GUI)

• click the first icon (OpenNRRD) and then select your NRRD data file
  
• click the Protocol tab
  
• click the Default button (near the tab) to create a protocol
  
• click RunByProtocol (bottom of window) to run the preprocessing
  
• when it finishes you can use GUI tools to see a report (you are on your own there)
  
• close the GUI
  

* you should now see a new …QCed.NRRD file with your results
* use nrrd2bxh to create a BXH header for your new NRRD file

The resultant DTI dataset's BXH header can then be used for DTI fiber tracking using either bxh_rundtk or bxh_runmedinria.

Analysis - Go back to Analysis software page

DTIPrep: quality control of diffusion-weighted images, Frontiers in Neuroinformatics, 2014
DTIPrep Tutorial, NA-MIC 2013