Hi Jose
If you add the --omatrix1 flag to probtrackx, it will output a matrix that counts the number of streamlines between any pair of voxels in your seed mask. So if your seed mask is the summation of all your masks, you will be able to extract the connectivity information between your N masks by summing across the appropriate rows of the matrix, without the need to run probtrackx N times.
What you will *not* be able to do is have these masks as termination masks as well (i.e. inforce that the streamlines do terminate when they reach one of the masks), because then none of the streamlines will even leave the seed voxels.
cheers,
Saad.
On 11 Mar 2011, at 12:13, Jose Angel Pineda Pardo wrote:
> Hi everyone,
>
> Im working with brain connectivity, and Im trying to build a connectivity matrix between a number of structures of the brain, all of them defined as region of interest in different nifti files.
>
> My question is about the execution time, because I want to be sure that Im doing it well. The pipeline is the next:
>
> Execution of BedpostX (takes about 4 hours for 1 fiber orientation)
> I build my different ROIs on the diffusion space, and generate the nifti files.
> And finally, execution of ProbTrackX as follows.
> From Multiple masks (all ROIs) to a termination mask. I will perform that N times, 1 for each possible termination mask. And finally, merging all the numbers from the "waytotal" file in the ProbTrackX I create my connectivity matrix. The problem is that each execution for a single termination mask takes about 24 hours, so it will take 90 days for creating the matrix between 90 masks. Is it that correct? Another cheaper possibility for performing that process.
>
> Thanks a lot
>
> Cheers
>
> Jose
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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