[Camino-users] probabilistic tractography

Mojdeh Zamyadi mojdehzm at gmail.com
Thu Apr 25 07:12:46 PDT 2013 

tried it with the brain mask:

track -inputfile DTI_ec_VoxelOrder.Bfloat -inputmodel bayesdirac
-schemefile bvec_rot.scheme -iterations 50 -seedfile aal_affine.nii.gz
-brainmask B0_brain_mask.nii.gz>  bayesianTracts.Bfloatand

and still get the following:

...
1917    0.9979156
1918    0.9984359
1919    0.9989562
1920    0.9994765
1921    0.9999968

Apr 23, 2013 6:50:34 PM misc.LoggedException logException
SEVERE: Exception in thread "main" class misc.LoggedException: target
value (0.9999972) is greater than CDF of all vectors in voxel 164 194 38
     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
(0.9999972) is greater than CDF of all vectors in voxel 164 194 38
     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)


any idea what might be going wrong? it's actually stock in Processing
ROI 1 of 116!

Thanks,
-M

On 04/23/2013 04:01 PM, Philip Cook wrote:
>  Try adding a brain / background binary mask with -brainmask
>
>  Sent from my iPhone
>
>  On Apr 23, 2013, at 12:49 PM, Mojdeh Zamyadi<mojdehzm at gmail.com>   wrote:
>
>>  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
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