[Camino-users] probabilistic tractography

Fri Apr 26 09:59:36 PDT 2013

Sorry for bombarding you with questions! I tried the same command on 
another subject and I get the same error (at the same spot)! So, this 
means it's probably not the subject but something with either the AAL 
atlas mask or the command options. Once again I greatly appreciate your 
input since I have no idea how to proceed from here! :(

Thanks,
-Mojdeh

On 04/25/2013 10:12 AM, Mojdeh Zamyadi wrote:
>
> 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
>>>>>>  http://www.nitrc.org/mailman/listinfo/camino-users
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>
>