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--- biac:dtiprep [2014/07/29 19:19]
voyvodic created
+++ biac:dtiprep [2023/02/23 18:43] (current)
@@ Line 1: / Line 1: @@
-DTIPrep
+===== DTIPrep =====
-On HUGIN:
+Minimal instructions:
- * 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)
+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]]

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