CINCH Tutorial

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CINCH and QUENCH are tools for interacting with estimated fiber tracts. These tools are designed to work well with mrDiffusion and ConTrack. They can also be used as stand-alone applications. This page is a tutorial the explains the interface. We assume you have downloaded the executable for your machine as well as the sample data set as explained on the CINCH and QUENCH pages.

Contents

[edit] Overview

We need to explain the modes of using CINCH and QUENCH here. They can be used in close coordination with mrDiffusion or in stand-alone mode.

[edit] Preparing data

We need to explain how to prepare the data separately for each of these modes.

1. If you use the updated dti preprocessing stream (specifically, if there is a \bin with nifti files inside the directory where your dt6 lives), and if you only plan to use Cinch to segment fibers tracked with mrDiffusion, then the only thing you may wish to do is copy the t1.nii.gz file from subjDir\t1\t1.nii.gz to subjDir\dti06\bin\t1.nii.gz. If you skip this step, cinch will still work well, but the background will be your B0 image. Its nicer to use the t1 as background.

2. If your dt6 was created in ancient history, the following functions might be useful for converting the dt6 to files usable by Cinch: dtiConvertDT6ToBinaries(). If the current version of CINCH does not work with your old dt6, try older versions available from our software page.

3. (Optional): To create the set of all fibers for use with CINCH use the Matlab script

  dtiTrackAllFibers()

You control the spacing distance for seed points - 2 mm is recommended for most tasks. One most of our local machines, this step takes about 5 minutes.

4. (Optional): Compute the distance matrix for a set of pathways. Computing a distance matrix makes it possible to interactively grow or shrink pathway selections. Use the Matlab script

 dtiComputePathwayDistanceMatrixForSelection()

5. (Optional): Create additional pathway selections by intersecting (ANDing) a single ROI with a pathway selection. If you are having trouble loading all the pathways into CINCH and want to limit your analysis to a smaller set, this is helpful. Use the Matlab script

dtiGenerateFiberSelectionFromRoi()

[edit] Loading data

CINCH uses its own 'pdb' file format. We convert fiber tracks estimated in mrDiffusion to the 'pdb' format. Normally, though, MrDiffusion reads and writes files in Matlab format.

There is good coordination between mrDiffusion and CINCH, but they are separate applications with different functions.

We create and measure fibers and diffusion data in MrDiffusion (or ConTrack). For example MrDiffusion measures diffusivity along the path, path length, and so forth.

CINCH is an interactive visual fiber group editor; We exchange fibers between CINCH and MrDiffusion for the purpose of efficiently editing and labeling fiber groups.

[edit] Using Cinch to segment fibers created in mrDiffusion

1. Generate the fiber group in mrDiffusion (e.g., track fibers from the left hemisphere and intersect them with the callosal ROI). If you are using the Cinch test data, try loading the CC fibers.

2. Remove from the mrDiffusion GUI all fiber groups except the ones that you wish to segment in CINCH.

3. Use the pulldown: "View | CINCH | Push current paths". You will queried whether you want to over-write the current CINCH paths. Say yes. The CINCH screen should load the fibers and look something like

After you finish your work in CINCH:

4. remove all fiber groups from mrDiffusion

5. Use the pulldown: "View | CINCH | get current paths" to move the edited groups from CINCH into mrDiffusion.

The distinct groups you created in CINCH will have the same colors and numbers in mrDiffusion.

N.B. On Linux, it is possible to save the fiber state and fibers directly as 'pdb' files and a cinch state file (cst). You can then open these directly the next time you invoke CINCH. There is, however, a CINCH bug on Windows platform: 'pdb' fibers are not saved properly from within CINCH. The work-around is to push the fibers from CINCH into mrDiffusion and save them using the pulldown 'File | fibers | Export current fibers'

[edit] Using Cinch as standalone application

If you have already saved fiber paths in CINCH, they will be in the 'pdb' format. You can then simply view and edit the existing fibers.

Step 1: Load the background

    File | Load Backgrounds
    This is usually a t1 or a vRGB map, with direction information.
    If you used dtiConvertDT6ToBinaries, the data is probably located in a bin/ directory underneath the directory that contained the DT6 file. You can also set the datapath by dragging this directory onto the application icon when you start it up.

Step 2: Load the pathways

    There are few ways to do this.
    (1) If you have previously saved fibers in CINCH, or exported fibers from mrDiffusion, in .pdb format you can simply go to File | Load Pathways.
    (2) If the pathways you want are in mrDiffusion, you can use mrDiffusion to "push" the paths to CINCH (via the View | CINCH | Push Paths command in mrDiffusion).
    (3) Alternately, if you used dtiTrackAllFibers() to compute the pathways and they were saved in .pdb, then you can also load them using the File | Load Pathways command.

Step 3: Load the State File (Optional)

    File | Load State
    The state file saves the "state" of a project so that you can keep working on it or load it at another time. Note that when you save a state file the fibers are not saved with it, only the bin assignments (0-8) are saved. You must first load the pathways, then load the state file (.cst).

[edit] Additional CINCH Tutorial Resources

See the paper website for descriptions of the interface, and a short movie showing examples of its use. Here is a link to using CINCH for performing corpus callosum parcellations. It provides some techniques for using CINCH to segment many fibers out of one large group. [1]

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