[Camino-users] probabilistic tractography

[Mojdeh Zamyadi]

so I tried the following command (where, "aal_affine.nii.gz" is the AAL 
template with 116 regions, non-linearly registered to the DTI space)

track -inputfile DTI_ec_VoxelOrder.Bfloat -inputmodel bayesdirac 
-schemefile bvec_rot.scheme -iterations 50 -seedfile aal_affine.nii.gz > 
bayesianTracts.Bfloat

and I got this error at the end:

1920    0.9994765
1921    0.9999968

Apr 23, 2013 8:48:58 AM misc.LoggedException logException
SEVERE: Exception in thread "main" class misc.LoggedException: target 
value (0.9999989) is greater than CDF of all vectors in voxel 143 160 61
     at 
tractography.BayesDiracRandomizer.getRandomizedPDs(BayesDiracRandomizer.java:223)
     at 
tractography.BayesDiracRandomizer.getRandomizedPDs(BayesDiracRandomizer.java:240)
     at 
tractography.BayesDiracTractographyImage.setVectors(BayesDiracTractographyImage.java:89)
     at 
tractography.ProbabilisticTractographyImage.getPDs(ProbabilisticTractographyImage.java:72)
     at 
tractography.NearestNeighbourInterpolator.getTrackingDirection(NearestNeighbourInterpolator.java:36)
     at 
tractography.EulerFibreTracker.getNextStep(EulerFibreTracker.java:57)
     at tractography.FibreTracker.trackFromSeed(FibreTracker.java:353)
     at tractography.FibreTracker.trackFromSeed(FibreTracker.java:230)
     at apps.StreamlineTractography.execute(StreamlineTractography.java:946)
     at apps.EntryPoint.main(EntryPoint.java:284)

Exception in thread "main" misc.LoggedException: target value 
(0.9999989) is greater than CDF of all vectors in voxel 143 160 61
     at 
tractography.BayesDiracRandomizer.getRandomizedPDs(BayesDiracRandomizer.java:223)
     at 
tractography.BayesDiracRandomizer.getRandomizedPDs(BayesDiracRandomizer.java:240)
     at 
tractography.BayesDiracTractographyImage.setVectors(BayesDiracTractographyImage.java:89)
     at 
tractography.ProbabilisticTractographyImage.getPDs(ProbabilisticTractographyImage.java:72)
     at 
tractography.NearestNeighbourInterpolator.getTrackingDirection(NearestNeighbourInterpolator.java:36)
     at 
tractography.EulerFibreTracker.getNextStep(EulerFibreTracker.java:57)
     at tractography.FibreTracker.trackFromSeed(FibreTracker.java:353)
     at tractography.FibreTracker.trackFromSeed(FibreTracker.java:230)
     at apps.StreamlineTractography.execute(StreamlineTractography.java:946)
     at apps.EntryPoint.main(EntryPoint.java:284)


Could you please help me with why I'm getting this?

Thanks,
-M

On 04/23/2013 12:19 PM, Mojdeh Zamyadi wrote:
> Thanks for the reply! Based on what I read, it means that I can use 
> the whole atlas, right? no need to produce separate seed regions, am I 
> right?
>
> On 04/23/2013 11:13 AM, Philip Cook wrote:
>> I'm at ismrm right now so apologies for the brief reply. Please see 
>> the man page for conmat
>>
>> Sent from my iPhone
>>
>> On Apr 23, 2013, at 9:03 AM, Mojdeh Zamyadi<mojdehzm at gmail.com>  wrote:
>>
>>> Hi all,
>>>
>>> I want to perform probabilistic tractography using Camino to 
>>> construct connectivity matrices. To do this I'm using the AAL 
>>> template with more than 100 cortical and subcortical regions. I've 
>>> transformed the AAL VOIs into the DTI space of each subject using 
>>> linear and nonlinear registration. My question now is, should I use 
>>> "track" command with "-inputmodel bayesdirac" option and use the 
>>> whole transformed AAL atlas as seedfile (eg. -seedfile 
>>> Control/aal_ROIs/aal_tformed.nii.gz)? Or should I create separate 
>>> mask/seed images for each region and perform the tractography for 
>>> each seed? Also, how can I get the the tracks between two seed 
>>> regions? Your help would be greatly appreciated!
>>>
>>> Thanks as always,
>>> -Mojdeh
>>> _______________________________________________
>>> Camino-users mailing list
>>> Camino-users at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/camino-users
>