TrackVis

Installation Problem (2015-08)

The diffusion toolkit replaces the Windows path with "C:\Program Files (x86)\Diffusion Toolkit" instead of append to the existing path. To fix this, you need to add "C:\Windows\System32" and "C:\Windows\SysWOW64" back to the path.

Windows 7 

1. From the Desktop, right-click the Computer icon and select Properties. If you don't have a Computer icon on your desktop, click the Start button, right-click theComputer option in the Start menu, and select Properties.
2. Click the Advanced System Settings link in the left column.
3. In the System Properties window, click on the Advanced tab, then click theEnvironment Variables button near the bottom of that tab.
4. In the Environment Variables window (pictured below), highlight the Path variable in the "System variables" section and click the Edit button. Add or modify the path lines with the paths you want the computer to access. Each different directory is separated with a semicolon as shown below.
   
   C:\Windows\System;C:\Windows\SysWOW64;C:\Program Files (x86)\Diffusion Toolkit

Converting to TrackVis format from SPM-converted

• locate raw files, as created by SPM conversion.

For example,:
V:\OSAHF2006\DTIpreprocess\CONTROL\CON131\DTI4series\dw_realign
Note: the "ar..." files have the basic preprocessing, namely converion, realignment ("r" - of b0 images in each series), and b0 errors ("a" - voxels where b0 < dw).

• create a folder to save the TrackVis files in; make sure this has the subject name, as the created files all have the same name ("niftiIN...nii").

• From the CSPM GUI, DTI Menu => 'Create TrackVis files"

• Select all the DTI files from the subject folder

Tip: in the spm_select GUI, use "^" to filter by the first letters in the file name, so "^ars.*"; then you can right-click and "Select All"

• Select the output folder

• You can run the processing by clicking on the link in the matlab command window

TrackVis Basics

File > Open Track > select file File > Load Image > select image (.nii) you wish to use, e.g. adc, b0, dwi, fa. (This step can be repeated to load multiple images) In panel on the upper right hand corner of the screen, R-click over 'Track 1' > Delete

Placing ROIs and Creating Tracks In bottom panel, under ROI, click on the icon > sphere. The sphere will appear where the crosshairs are, and can be shifted into place manually in the sagittal, coronal and axial views.

In main view, R-click over sphere > Create New Track Group. Edits can be made to the track in the Property panel (bottom right corner of screen) - e.g. change name, length threshold (changing the 'low' to 10mm excludes the tiny fibers), apply ROI filters (see below)

Multiple spheres can be used to create a track. In panel on the upper right hand corner of the screen, R-click over 'Track 1' > Toggle Existing ROI > select desired sphere/ROI In the Property panel, select Track tab > expand information for each sphere by clicking on the triangle, to expose operators. These can be changed to filter out certain fibers - e.g. if the operator is 'and' for each sphere, only fibers which pass through BOTH spheres will remain... if you change one to 'not', it will exclude any fibers which pass through that sphere.

Track information (i.e. mean length, adc, fa) is displayed at the bottom of the Property panel. Click on 'view' to see more detailed information (i.e. min an max length, histogram).

File > Save Scene As > name file and location. (This will save everything - tracks, ROIs, loaded images)