JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  June 2012

FSL June 2012

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: probtrackx2 and omatrix1

From:

Sourena Soheili <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 14 Jun 2012 19:50:56 +0430

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (164 lines)

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
>

Top of Message | Previous Page | Permalink

JISCMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


WWW.JISCMAIL.AC.UK

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager