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From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Friday, November 11, 2011 4:45 PM
Subject: Re: [Freesurfer] DTI Group Analysis Study


1. Currently trac-all uses only the MNI template, not CVS. So yes, all
  steps apply.

2. See the tracula tutorial, section "outputs from tracula", to see where
  to find the MNI-space outputs.

3. What clusters are you talking about? Do you want to do a voxel-based
  analysis? If so, why are you using tracula? Go through the tracula
  tutorial and read the tracula paper below to understand what tracula
  does:
  http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract

On Fri, 11 Nov 2011, Antonella Kis wrote:

> Hi,
>
>
> I am trying to do a DTI Group Analysis study using a MNI152 standard space
> for registration.
>
>
>
> 1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA
> if I have to follow all the steps 
>
>    starting Setting Up a Configuration File to run Tracula and then to 
> continue with the following three steps in the TRACULA processing stream
> (which is called by the command trac-all):
>  *  Pre-processing
>  *  FSL's bedpostX
>  *  Reconstructing white-matter (WM) pathways
> 2). Can I check the registration for individual subjects to see if it worked
> well or not on the MNI 152 template?
>
>
> 3) How can I  see if there are clusters that survives to multiple comparison
> in group 1 (controls) versus group 2 (patients) without and covariant (not
> gender, not age).
> Can I get a txt file as output for this clusters?
>
>
>
> Thank you.
> Antonella
>
>
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