Converting BRIK file to text file
- Go to directory with your BRIK and header files.
- Run afni
Click "Define Datamode > plugins > Diffusion"
- Click Choose Diffusion Dataset and select a +orig file (it must have a corresponding header file also)
- If the diffusion tensor is already calculated click "Choose FTM (DTI) Dataset" and select your DTI file
- Otherwise hit "Diffusion Tensor" and "Compute" which should generate a DTI file in your directory
- Click "Done" in the diffusion plugin window.
In the main AFNI window click "plugins > Dump 3D 98"
- For 3D brick choose the DTI file (probably use the same one as before)
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.
- Click "Threshold Mask" and specify a range. We used .0001 and 1.0
- Specify an output filename as well.
- Click Dump+Close
- Close AFNI, and you should find the output filename you selected in your current directory.
Visualize in 3D with afni
- From the diffusion pluggin
- Choose Diffusion Dataset like before
- Load Anatomical dataset (the file without DTI extension)
- Click "Initiate"
- Change "Axial" Slicer to view different layers in stack
Visualize primary eigenvectors in afni
- Perform same steps as above
- Lower FAI thresh to around 0.2
- Try clicking Vector Field Ax1 or Colormap on Slice Ax1. One of these should enable the eigen vector.