Brain Imaging & Analysis Center

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===== 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

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