Installing and Using DTI-Query and/or CINCH (in 4 steps)

1. Decide which software you need (DTI-Query and/or CINCH).
   

   In DTI-Query, pathways are selected by interactively specifying "volumes of interest," and finding the pathways that intersect these regions. CINCH takes a different approach - pathway selections are specified using sequences of mouse gestures, which gradually segment the white matter pathways.

   In our lab at Stanford, we've found DTI-Query more useful during the initial exploratory stages of an investigation. CINCH has been more useful when the task is known (for example, segmenting a known set of pathways into anatomical groups). CINCH has also been useful for preparing images for publication, since it makes it easy to remove pathways that are clearly the result of tractography errors.

   You may want to try them both before you decide.

2. Obtain the software.
   

   Download a precompiled binary for your platform.
   
       -or-
   
   Download the source code and build it yourself.(CINCH source coming soon!)
   
       -or-
   
   Download and build it using a MacPort or FreeBSD port (DTI-Query only).
   

3. Preprocess your data.
   
   Learn how to process your data.
   

   Download sample data from our papers.
   

4. Analyze your data!
   
   Start by running the dtiquery or CINCH application. You can load background images and pathways using commands under the 'File' menu. (Shortcut: If you supply a directory on the command line, all the background images in this directory will automatically be loaded.)

   Here are some resources for learning DTI-Query and CINCH:

   Papers:

   Original DTI-Query paper (Akers et al., '04)

   CINCH paper (Akers, '06)

   Videos:
   DTI-Query video (5 minutes, 232 MB quicktime .mov)

   CINCH video (5 minutes, 29 MB quicktime .mov)

   Note that the sample data for DTI-Query and CINCH come with state files (*.qst and *.cst) that enable you to (approximately) reproduce some of the figures from each paper. You can load any of these after you have loaded the pathways and the background image(s).