===== DTIPrep =====

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 **[[biac:dtk|bxh_rundtk]]** or **[[biac:medinria|bxh_runmedinria]]**.


[[biac:analysis|Analysis]] - Go back to Analysis software page

[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906573/|DTIPrep: quality control of diffusion-weighted images, Frontiers in Neuroinformatics, 2014]]\\
[[https://www.slicer.org/slicerWiki/images/a/a6/DTIPrep_TutorialContestSummer2013.pdf|DTIPrep Tutorial, NA-MIC 2013]]