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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