[Camino-users] newbie question

[Alexandra Badea]

Thank you very much Phil!
Will makers my input data is masked, and will look into -inputmodel
bayesdirac_dt!

Alex

On 12/19/14 9:59 AM, "Philip A Cook" <cookpa at mail.med.upenn.edu> wrote:

>Hi,
>
>These happen when the ball and stick model optimization fails to converge
>in a voxel. If the tracts are getting outside the brain at all, then you
>will see a lot of these. This can be prevented by using a brain mask.
>Otherwise, the occasional failure can happen but if you are seeing
>hundreds of them, something else might be wrong.
>
>You can also try
>  
>  -inputmodel bayesdirac_dt
>
>this uses a linear model (a cylindrical tensor) to estimate the
>probability of each orientation within the voxel.
>
>On Dec 11, 2014, at 3:02 PM, Alexandra Badea <alexandra.badea at duke.edu>
>wrote:
>
>> Greetings!
>> 
>> Thank you for sharing the camino tools! I have tried to follow the
>>tutorial for tracking and use the test data provided. I have used
>>itksnap to generate a rather rough ROI and then called track, when I get
>>warnings like these:
>> 
>> 1. 
>> Processing seed 502 of 1275optimizers.MarquardtMinimiserException:
>>Infinite objective function in mrqcof.
>> optimizers.MarquardtMinimiserException: Infinite objective function in
>>mrqcof.
>> optimizers.MarquardtMinimiserException: Infinite objective function in
>>mrqcof.
>> 
>> 
>> And
>> 2. 
>> 
>> optimizers.MarquardtMinimiserException: Singular Matrix in gaussj - 2
>> 
>> 
>> I would very much appreciate your help in understanding this messages,
>>and if there is something I can do about it!
>> I have the feeling it might have to do with ROI definitionŠ
>> 
>> With best wishes & Many thanks!
>> 
>> Alexandra
>> 
>> ****
>> PS: attaching the call to track:
>> 
>> rhodos:alexplay alex$
>>/Applications/SegmentationSoftware/camino-code-163f67cbf550560aa351b3d0a3
>>bbbd7a22863cb4/bin/track -inputfile dwi.Bfloat -inputmodel bayesdirac
>>-schemefile 4Ddwi_b1000_bvector.scheme -iterations 50 -seedfile
>>/Volumes/alex_home/braindata/camino_testdata/example_dwi/brain_mask.nii.g
>>z > bayesianTracts.Bfloat
>> 
>> Dec 11, 2014 2:00:02 PM apps.StreamlineTractography initVariables
>> INFO: Defining input physical space from seed file
>> Dec 11, 2014 2:00:07 PM tractography.BayesDiracRandomizer <init>
>> INFO: Allocating space to cache 56162 likelihood functions
>> Processing ROI 1 of 1
>> 
>> 
>> 
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>