Hi - you can do this by running probtrackx2 with the --network option on, and regions A and B as two separate seed masks/surfaces. These should be entered as a text file that contains paths to the relevant files. The result will be the connection maps from A to B and from B to A added together.

Cheers
Saad

On 14 Jun 2012, at 13:04, Sourena Soheili wrote:

> Dear Saad
> Suppose we have a disease condition which disrupts connectivity of
> cortical region A to B. We run probtrackx with Matrix1 to record
> repertoire of cortico-cortical connectivity information in patients
> group as well as healthy controls, and run t-statistics. So the
> omatrix1 is converted to a statistical significance map with the same
> dimensionality.
> This map only encodes cortical regions A and B (as thresholded
> significant mesh vertices), not the underlying tracts which are
> influenced by the disease condition.
> So I am seeking a solution to visualize the tracts which show a
> disease-related impact.
> 
> I wonder what is the best approach to span over all streamlines like this:
> 
> For each #voxel in Significant_Matrix_1; Do
> Let foo = seed voxel associated to #voxel
> Let bar = target voxel associated to #voxel
> Run probtrackx with options seed=foo target=bar
> Done
> Sum up all tractograms associated with NxN vertex connections
> 
> 
> On 6/14/12, Saad Jbabdi <[log in to unmask]> wrote:
>> Not sure I follow you. I guess you want to track from specific vertices
>> (depending on the results of some analysis).
>> You can do that by setting the scalar values of your seed surface to 1's and
>> 0's.
>> 
>> Saad
>> 
>> On 13 Jun 2012, at 22:53, Sourena Soheili wrote:
>> 
>>> Hi Saad
>>> Consider some manipulation is performed on raw matrix1 (e.g. groupwise
>>> comparisons and zeroing of the non-significant connections, or a
>>> simple segmentation). Is there a method to feed the manipulated
>>> matrix1 into the probtrackx pipeline and visualize the tractogram
>>> which renders only the significant connections? (The only option which
>>> comes to my mind is vertexwise reading of connections-of-interest from
>>> manipulated matrix1 and then performing separate vertex-to-vertex
>>> tractographies and lastly summing up all the results.)
>>> 
>>> Is there a better option available?
>>> 
>>> Cheers,
>>> Sourena
>>> 
>>> On 6/12/12, Saad Jbabdi <[log in to unmask]> wrote:
>>>> Yes.
>>>> 
>>>> 
>>>> On 12 Jun 2012, at 14:19, Sourena Soheili wrote:
>>>> 
>>>>> Hi Saad
>>>>> Is the NxN matrix arranged based on vertex numbers (as extracted from
>>>>> the source mesh topology file) in every dimension?
>>>>> 
>>>>> Thanks,
>>>>> Sourena
>>>>> 
>>>>> 
>>>>> On 6/12/12, Saad Jbabdi <[log in to unmask]> wrote:
>>>>>> Hi
>>>>>> If the seed mask is a surface omatrix1 will encode vertex-to-vertex
>>>>>> connectivity of the seed mask. Dimensions are NxN where N is the
>>>>>> number
>>>>>> of
>>>>>> vertices.
>>>>>> Detection of surface crossing is done using triangles, then the
>>>>>> nearest
>>>>>> vertex within the crossed triangle is considered for counting.
>>>>>> 
>>>>>> Cheers
>>>>>> Saad
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 11 Jun 2012, at 20:21, Sourena Soheili wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> I have a few questions about probtrackx2 and --omatrix1 option,
>>>>>>> If a triangular freesurfer surface is used as a seed mask, does the
>>>>>>> omatrix1 encode "triangle" to "triangle" surface connectivity
>>>>>>> information?
>>>>>>> (I've seen in a previous post that it is not a vertex-wise matrix)
>>>>>>> 
>>>>>>> What will be the dimensionality of the omatrix1 nifti file?
>>>>>>> 
>>>>>>> Is it correct that the seed/target voxels in each nifti dimension are
>>>>>>> arranged and ordered by their #face or #vertex in the input mesh?
>>>>>>> Thanks in advance,
>>>>>>> Sourena Soheili
>>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> 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
>>>> 
>>> 
>> 
>> --
>> 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