[Camino-users] probabilistic tractography
Mojdeh Zamyadi
mojdehzm at gmail.com
Mon Apr 29 08:12:57 PDT 2013
Thanks so much for the reply. So should I re-install Camino?
This is a warning I get quite frequently :
"Processing seed 13093 of 14773optimizers.MarquardtMinimiserException:
Infinite objective function in mrqcof.
optimizers.MarquardtMinimiserException: Infinite objective function in
mrqcof."
what does this exactly mean? is it fine to get this type of warning?
-Mojdeh
> On 04/29/2013 10:54 AM, Philip A Cook wrote:
>> No worries, it is a legit bug. It happened because the likelihood of
>> all directions in the voxel did not sum precisely to 1.
>>
>> I have increased the epsilon in r1205 so hopefully this problem
>> should go away. You might see a warning about sampling failure, but
>> this should happen very infrequently. If it does, the program should
>> just use the maximum likelihood vector and carry on, rather than
>> crashing.
>>
>>
>> On Apr 26, 2013, at 12:59 PM, Mojdeh Zamyadi wrote:
>>
>>> 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
>>>>>> _______________________________________________
>>>>>> Camino-users mailing list
>>>>>> Camino-users at www.nitrc.org
>>>>>> http://www.nitrc.org/mailman/listinfo/camino-users
>>>>
>
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