R: [Camino-users] tractography error

[Philip A Cook]

I've added a fix of sorts. Seeds outside the diffusion image will now be ignored, so it won't crash. This shouldn't be a problem for procstreamlines with -outputacm, but it might cause trouble for seed-based probability maps because the seed image and the output tracts will be out of sync due to the missing seed points.

This may cease to become an issue in the future when the tracking algorithms are updated. Meanwhile the best suggestion I can make is to ensure that seed points are inside the image volume where you want to track. 


On Jul 5, 2012, at 10:55 AM, Curci Marina Carmela wrote:

> Good morning,
> I would like to know if you have found a solution for my problem.
> With the header of another subject I don't have problem but obviously the final output doesn't match the T1 image.
> Could you give me some suggestions or help, please?
> 
> Thank you for your availability,
> Marina
> 
> ________________________________________
> Da: Philip A Cook [cookpa at mail.med.upenn.edu]
> Inviato: venerdì 29 giugno 2012 21.20
> A: Curci Marina Carmela
> Cc: camino-users at www.nitrc.org
> Oggetto: Re: [Camino-users] tractography error
> 
> Hi,
> 
> I think that some of your seed points are outside the diffusion image volume. I will update the code to deal with this.
> 
> On Jun 28, 2012, at 9:32 AM, Curci Marina Carmela wrote:
> 
>> Hello to everyone!!
>> I'm using Camino to do tractography.
>> I did a lot of tests to learn how to use it, but today I have an error that I've never had during deterministic tractography. It seems that there are 9411 seeds in the voxel instead of 9416.
>> 
>> 
>> track -inputfile tensor.Bdouble -inputmodel dt -header DTI.nii.gz -seedfile bin_reduc_seedROI_8.nii.gz -outputfile tracks_bin8.Bfloatt
>> Jun 28, 2012 3:26:53 PM apps.StreamlineTractography initVariables
>> INFO: Defining input physical space from DTI.nii.gz
>> Jun 28, 2012 3:26:53 PM imaging.ImageHeader sameDimensions
>> INFO: Data dimensions differ between bin_reduc_seedROI_8.nii.gz and DTI.nii.gz
>> Processing ROI 1 of 1
>> Processing seed 9411 of 9416
>> 
>> Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 34
>>      at tractography.TractographyImage.numberOfPDs(TractographyImage.java:155)
>>      at apps.StreamlineTractography.execute(StreamlineTractography.java:891)
>>      at apps.EntryPoint.main(EntryPoint.java:275)
>> 
>> How could I solve this problem please?
>> It is very urgent, please!!
>> Thank you very much,
>> Marina_______________________________________________
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>