Process raw DTI data in DTI Studio

Written by Owen Phillips. Email if you have any questions. This protocol explains how to process raw Siemens Dicom data in DTIStudio. For more information on identifying white matter tracts using DTIStudio, see http://www.loni.ucla.edu/~narr/protocols.php or the related protocols belows.

Note: Tractography shown in this protocol was performed in DTIStudio using 30 direction diffusion data.

1. Open DTI Studio.
2. Go to File, and select DTI Mapping. Select "Siemens, GE or Philips DICOM".
   
   
3. For DTI parameters select. Slice orientation = Axial. Slice Sequencing = Inferior-superior, Slices to be processed = All Slices, b_value = 1000. Copy and paste in the following Gradient Table:
   
   1:0,0,0
   2:0,0,0
   3:0,0,0
   4:0,0,0
   5:0,0,0
   6:-1,0,0
   7:-0.166,0.9862,0
   8:0.11,0.6639,0.7398
   9:-0.9012,-0.4191,-0.11
   10:0.1691,-0.601,0.7812
   11: 0.8148,-0.3858,0.4329
   12:-0.656,0.3661,0.6601
   13:-0.5822,0.8004,0.1431
   14:-0.9001,0.2591,0.3501
   15:-0.6932,-0.6983,0.1781
   16:-0.3568,-0.9236,-0.1399
   17:-0.5431,-0.4881,-0.6831
   18:0.5252,-0.3961,0.7533
   19:0.6393,0.6893,0.3412
   20:0.33,-0.0129,-0.9439
   21:0.5241,-0.783,0.3351
   22:-0.6087,-0.0649,-0.7906
   23:-0.22,-0.233,-0.9472
   24:0.004,-0.9098,-0.4149
   25:0.5108,0.6267,-0.5886
   26:-0.4138,0.7368,0.5348
   27:0.679,0.139,-0.7209
   28:-0.8839,-0.2959,0.362
   29:-0.2619,0.432,0.863
   30:-0.0879,0.185,-0.9787
   31:-0.2939,-0.9068,0.302
   32:-0.887,-0.089,-0.453
   33:-0.2569,-0.4429,0.859
   34:-0.0859,0.867,-0.4909
   35:-0.8632,0.5042,-0.026
   
   
   Select "Dicom Image-Files Folder" - This will be your raw Dicom DTI data. Select file "1". DTIStudio will read in all the files even though you have only selected the first.
   
   
4. Click on DtiMap
   
   
5. Select "Calculation - Tensor, Color Map etc. The default settings will be set and should be used but they are as follows: Create a mask-image based on the background noise level: 10 Consider B-Value Use the mean B0 of all scans for DTI calculation (default) Standard SVD method for LMS equation (default).
   
   Click "Ok".
6. You will get a prompt "Automatic Outlier Rejection?" Click Yes.
7. You will get a prompt "DTI-Map Options: Automatic Outlier Rejection. Keep the default settings.
   Tensot quality feature: Regular difference between the Fitting and the Original images, Criterior to judge a bad image: Auto-correlation: 2-pixels lag - Threshold: 2.2, Action on the bad images in each iteration: Reject the worst one. Verify the result: For the iteration 1.
   
   
8. Click on Fiber Tracking.
   
   
9. You will get a prompt: "Fiber-Tracking Parameters". Set "Start Tracking if Fractional Anisotropy > 0.2 and Stop Tracking if Fractional Anisotropy < 0.2 if Tract turning angle > 70.
   
   
10. Click on the Image Tab down at the bottom Right of the Program. Click on Image Processing - Color Map. Select Eigen Vector - 0 and Anisotropy - FA. Click Ok.
    
    
11. Click the bottom right tab - Fiber. Select the following options on the right hand command panel. Fiber Display = Selected, show fibers on 2D image. Fiber Selection = ROI - Drawing Enable. Fiber Color = Random. ROI - Shape = Free. ROI Operation = or.
    
    
12. Identify the Arcuate Fasciculus.
    

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