Hi
From --help command I understand that in --network mode any path which
touches at least one of the targets will survive. Now suppose we have
a segmented matrix1 which only encodes bilateral portions of the
corticospinal tract for hand movement, meaning that it only includes:
tract1: brainstem vertices to right hand motor cortex vertices
tract2: brainstem vertices to left hand motor cortex vertices
If I run in --network mode, won't I get some extra tracts connecting
right and left motor cortices?
(Please consider that the real scenario can be much more complicated,
and there could be no several "discrete" mesh patches to seed to/from,
rather, a single confluent mixure of thresholded matrix1 entries.)
What can be the best approach here?
Cheers,
Sourena
On 6/14/12, Saad Jbabdi <[log in to unmask]> wrote:
> 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
>
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