[Camino-users] newbie question

[Philip A Cook]

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 definition…
> 
> With best wishes & Many thanks!
> 
> Alexandra
> 
> ****
> PS: attaching the call to track:
> 
> rhodos:alexplay alex$ /Applications/SegmentationSoftware/camino-code-163f67cbf550560aa351b3d0a3bbbd7a22863cb4/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.gz > 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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