Thanks for the quick response, Saad! This worked on a test case.
One follow up question, is there a way to suppress writing all the "seeds_to_*.nii.gz" files? I won't need these and they are pretty big.
-Julia
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Saad Jbabdi [[log in to unmask]]
Sent: Thursday, October 25, 2012 9:13 AM
To: [log in to unmask]
Subject: Re: [FSL] obtaining an ROI to ROI connection matrix
HI Julia
You can create a ASCII list of your 82 ROIs and use the following options:
probtrackx2 --targetmasks=listOfTargets.txt --os2t --s2tastext [+all other options]
You will then get an output matrix in the form of an ASCII text file that has dimensions #seedVoxels X 82 which you can load in Matlab and sum along the 1st dimension.
It is then straightforward to concatenate the results across the 82 runs.
Cheers
Saad
On 25 Oct 2012, at 16:57, Owen, Julia wrote:
> Hi Saad and probtrackx users,
>
> I have been following the listserve and I don't think this exact question has been asked since the FSL5 release.
>
> I am running probtrackx2 with a number of ROI seed regions, 82 to be exact. To cut down on computation time, I parallelize over seeds, so I run 82 separate probtrackx2s on a grid. Is there a way to output a 1x82 vector, which is the sum of the connectivity between the seed region and all the 82 seed regions? Thus, by concatenating these vectors from the 82 runs, I could obtain the 82x82 connection matrix (ignoring the diagonal entries). I imagine that this might be possible given some combination of settings, but I can't figure out how to do it AND keep my probtrackx2 calls parallel.
>
> Currently, I just use a seed mask in probtrackx2 and then post hoc, I mask the FDT results with the 82 seed regions. This method works just fine, but I'd like to streamline the pipeline if the functionality is there.
>
> Thanks so much in advance.
>
> -Julia
--
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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