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
>
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