I am afraid not. sorry!
On 25 Oct 2012, at 17:37, Owen, Julia wrote:
> 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
> ________________________________________
> 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
>
--
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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