AFNI

Converting BRIK file to text file

1. Go to directory with your BRIK and header files.
2. Run afni

3. Click “Define Datamode > plugins > Diffusion”

4. Click Choose Diffusion Dataset and select a +orig file (it must have a corresponding header file also)
   1. If the diffusion tensor is already calculated click “Choose FTM (DTI) Dataset” and select your DTI file
   2. Otherwise hit “Diffusion Tensor” and “Compute” which should generate a DTI file in your directory
5. Click “Done” in the diffusion plugin window.

6. In the main AFNI window click “plugins > Dump 3D 98”

   1. For 3D brick choose the DTI file (probably use the same one as before)

   2. Click the SubBrik info checkbox, and specify subbrick threshold (19 appeared to be the FA; maybe this can be verified in the “Define Overlay” interface in the main AFNI window.

   3. Click “Threshold Mask” and specify a range. We used .0001 and 1.0
   4. Specify an output filename as well.
   5. Click Dump+Close
7. Close AFNI, and you should find the output filename you selected in your current directory.

Visualize in 3D with afni

1. From the diffusion pluggin
   1. Choose Diffusion Dataset like before
   2. Load Anatomical dataset (the file without DTI extension)
   3. Click “Initiate”
   4. Change “Axial” Slicer to view different layers in stack

Visualize primary eigenvectors in afni

1. Perform same steps as above
2. Lower FAI thresh to around 0.2
3. Try clicking Vector Field Ax1 or Colormap on Slice Ax1. One of these should enable the eigen vector.