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FSL  May 2009

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Subject:

Re: question re probtrackx network mode

From:

Saad Jbabdi <[log in to unmask]>

Reply-To:

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

Date:

Mon, 25 May 2009 08:37:13 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (220 lines)

Also, you can use a region as a waypoint, termination, and  
classification target at the same time. That way, you can get your  
quatitative comparisons from the seed_to_target files, and dissect  
your connection via waypoint/termination to check that it is  
anatomically reasonable.

Cheers,
Saad.

On 25 May 2009, at 05:48, Matt Glasser wrote:

> You might be better served by running seeds to targets mode using  
> each of
> your regions as a seed with the other two as targets.  This will  
> record the
> actual number of streamlines that go from each seed to each target,  
> which
> will allow you to make quantitative comparisons between the  
> strengths of
> each pathway.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On  
> Behalf
> Of Michael Scheel
> Sent: Sunday, May 24, 2009 10:46 PM
> To: [log in to unmask]
> Subject: Re: [FSL] question re probtrackx network mode
>
> Hi Saad, many thanks for the clarification - I see now why my
> suggestion makes little sense.
>
> Regarding my study - I tried the termination masks but realized this
> is not what I want to do. So here is what I want to do:
>
> I have Region A, B and C. I want to show connections between
> A and B,
> A and C,
> B and C (which I hope are not there according to the hypothesis)
>
> I'd like to also compare the connection strengths/probabilities for
> these connections in a number of subjects.
>
> Network-mode will give me Connections that pass through the regions,
> but I want them to end there.
> Termination masks will give me all connections from one region,
> including those that terminate in the target region - I want only
> those that terminate.
> Waypoint masks again will give connections that pass through.
> Exclusion masks is not what I want.
>
> So I'm a bit lost and start to wonder if that's what I want is a
> reasonable thing to do, or not? If it is reasonable, which I still
> hope - how would you suggest to do that?
>
> Thanks, Michael
>
>
> On 24-May-09, at 12:36 PM, Saad Jbabdi wrote:
>
>> Hi Michael,
>>
>> On 24 May 2009, at 19:07, Michael Scheel wrote:
>>
>>> Hi Saad, thanks for the answer. Some questions just to make sure
>>> that I understood correctly.
>>>
>>> I've often come across the symmetric mode (---mask2) in the
>>> discussions and I was assuming that this is something like:
>>>
>>> Track from RegionA to RegionB AND from RegionB to RegionA - only
>>> those tracts survive that fullfill both conditions. From your answer
>>> I understand that they don't necessarily have to take the same way.
>>> However - wouldn't that be a strong confirmation of the certainty of
>>> the tract travelling this route?  I guess depending on seed and
>>> target chances are sometimes low that one sample from AtoB has a
>>> counterpart BtoA and one would need a huge sample number to find
>>> those. One would have to store for every sample of seed region A the
>>> "voxelway" and then compare this with the table of voxelways from
>>> regionB. I guess the problem is how to visualize the results of this
>>> - hower just an idea.
>>
>>
>> There is no theoretical reason for accepting only sample tracts that
>> take the exact same route both ways. Remember: in probtrackx, we are
>> building a (spatial) histogram of connections using sampling. Each
>> sample is a random draw from that distribution. So, even if the
>> distribution that represents A->B is the exact same distribution as  
>> B-
>>> A, there is no reason why the samples should be the same..
>>
>>>
>>>
>>> My question really is for the symmetric mode. Does this show (as in
>>> network-mode) connections from A that pass through B AND connections
>>> from B that pass through A. Or is it connections from A that end in
>>> B AND from B that end in A.
>>
>> Network mode is exactly the same thing as symmetric mode, but  
>> extended
>> to more than two regions. I.e. if you use two regions in network  
>> mode,
>> you get the same answer as two masks symmetric.
>> The samples that are kept are the ones that pass through the target
>> regions (as opposed to "end in").
>>
>>
>>>
>>>
>>> Another question re the network mode:
>>> You said:
>>>> It will show you an overlay of the following three distributions:
>>>> . connections from A that pass through either B or C
>>>> . connections from B that pass through either A or C
>>>> . connections from C that pass through either A or B
>>>
>>> Is there an option of tracking:
>>> . connections from A that end in either B or C
>>> . connections from B that end in  either A or C
>>> . connections from C that end in  either A or B
>>> I guess I could use the target mode for every combination and
>>> overlay the results - correct? Is there already an option or script
>>> to automate this?
>>
>> You are probably thinking of using termination masks. Unfortunately,
>> you cannot use the seeds as terminations in network mode. You will
>> need to run probtrackx several times.
>>
>>>
>>>
>>>
>>> Thanks a lot, Michael
>>>
>>
>> Cheers,
>> Saad.
>>
>>>
>>> On 24-May-09, at 2:45 AM, Saad Jbabdi wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> On 23 May 2009, at 21:56, Michael Scheel wrote:
>>>>
>>>>> Hi fsl-gurus,
>>>>>
>>>>> I have 2 questions re the probtrackx network mode:
>>>>>
>>>>> Say I have a Region A, B and C defined as masks and enter them as
>>>>> Multiple seed masks.
>>>>> What connections will be shown to me:
>>>>> 1) Any connections between A and B, A and C, B and C or 2) just
>>>>> connections that connect all of them, i.e. A-B-C, A-C-B and B-A-C.
>>>>
>>>> neither exactly 1) nor exactly 2).
>>>> It will show you an overlay of the following three distributions:
>>>> . connections from A that pass through either B or C
>>>> . connections from B that pass through either A or C
>>>> . connections from C that pass through either A or B
>>>>
>>>>
>>>>>
>>>>>
>>>>> Assuming it is (1), and looking only at connections between A and
>>>>> B.
>>>>> As I understand from previous discussions, tracking samples are
>>>>> send
>>>>> from A to B and B to A and only those that reach their target in
>>>>> both conditions 'survive'.
>>>>> What I'm wondering about is what are the constraints regarding
>>>>> that:
>>>>> Does the sample has to go the exact same voxelway to be found  
>>>>> valid
>>>>> or is it rather an overlay where voxels survive that were passed
>>>>> from either direction, i.e. at least one sample passed from AtoB
>>>>> AND
>>>>> BtoA.
>>>>
>>>> It is the latter. A tract survives if it reaches its target,
>>>> regardless of the route it has taken.
>>>>
>>>> Cheers,
>>>> Saad.
>>>>
>>>>
>>>>>
>>>>>
>>>>> Thanks, Michael
>>>>>
>>>>
>>>> --
>>>> Saad Jbabdi
>>>> Oxford University FMRIB Centre
>>>>
>>>> JR Hospital, Headington, OX3 9DU, UK
>>>> +44 (0) 1865 222545  (fax 717)
>>>> www.fmrib.ox.ac.uk/~saad
>>>
>>
>> --
>> Saad Jbabdi
>> Oxford University FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> +44 (0) 1865 222545  (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>

--
Saad Jbabdi
Oxford University FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545  (fax 717)
www.fmrib.ox.ac.uk/~saad

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