FSL - probabilistic tracking

Owned by Jaimi Shepperd (Unlicensed)
Jul 15, 2013
1 min read

Preparing the images

  • Make sure the Linux Share is setup in CSPM -> Utilities -> Local settings.
  • Run CSPM analysis, and select the "FSL" option in the "Combined" pane, then run "Combined"; this will create DTI subfolders for each subject under the Linux share.


For Example: V:\LinuxShare\subjects4FSL\CCHS2002

Pre-processing

The first step in preparing DTI data for processing is called Bedpost processing.

The results of the Bedpost processing are stored in V:/LinuxShare (on the Linux computer, this directory is accessible as ~/mnt/hgfs/LinuxShare). The name of the folder containing the Bedpost results is called "subjectname.bedpostX" (eg. CCHS2002.bedpostX).

For more about Bedpost processing see the official FSL website for documentation.

Connections

To initiate probabilistic tracking in FSL:

  1. Open LinuxVM
  2. In the terminal window, type "fsl"
  3. In the FSL window, click "FDT diffusion"
  4. In the FDT diffusion toolbox window:
    • Select the bedpostX directory by navigating to the folder containing the bedpostX data for the corresponding subject (eg. CCHS2002.bedpostX)
    • Under seed space, select "single mask." This tells FSL to conduct probabilist tracking from a single user-defined VOI.
    • Under "mask image," select the VOI from which to run probabilistic tracking. The VOI must be in .nii format, and should be traced from the individual subject's normalized T1 image.
    • Do not check "seed space is not diffusion."
    • Manually create a new folder in the LinuxShare drive in which to store the processed results. Select this folder as the output directory.
  5. Press "go." If the program asks you whether to overwrite a file, click "yes."

Volume between structures