[Camino-users] connectivity analysis

[Philip A Cook]

Hi,

Without getting into details of study design, I can answer the questions about the tool itself:

You can use either deterministic or probabilistic tracking with conmat. The output will be the total number of streamlines that connect each pair of nodes, where a node is a region with a single integer label. 

The tutorial details a specific use case in which whole-brain tractography is combined with AAL labels. I have edited the text to make this more clear.

In order to preserve flexibility, conmat doesn't try to do anything clever with the streamline counts. It just reports how many lines connect each pair of regions. It's up to the user to normalize for the multiple factors (such as number of probabilistic iterations) that can affect these numbers. There's various graph-theory approaches to this, such as thresholding and binarizing the graphs at constant degree.


On Jan 21, 2014, at 11:35 AM, Mojdeh Zamyadi <mojdehzm at gmail.com> wrote:

> Hi all,
> 
> I have a few question regarding connectivity analysis using Camino. I want to create a connectivity matrix for 92 regions from AAL atlas (I've already nonlinearly registered and resampled the AAL atlas into each subject's DTI space). I've looked at the tutorial page: http://cmic.cs.ucl.ac.uk/camino//index.php?n=Tutorials.ConnectivityMatrices
>   
> and still have a few questions. Can I use probabilistic tractography (ie. track -inputmodel bayesdirac_dt) or deterministic tractography is good enough?! is there a point in doing the probabilistic tractogrtaphy (since it takes a lot of time!).  Also, it's mentioned in the page that "it is assumed that whole-brain tractography has already been performed", the command I was thinking of using is the following:
> track -inputfile DTI_ec_VoxelOrder.Bfloat -inputmodel bayesdirac_dt -schemefile bvec_rot.scheme -iterations 1000 -seedfile AAL_labels_to_DTI_resampled.nii.gz -brainmask B0_brain_mask.nii.gz -pointset 0 > bayesianTracts_1000.Bfloat
> 
> where my -seedfile is the 92 region AAL atlas which does not cover the whole brain! I though since I'm only interested in those ROIs, I can used that instead of whole brain ROI. Could someone clarify these points for me? 
> 
> Thanks a lot,
> -Mojdeh 
> 
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