[Camino-users] tractography

[Philip A Cook]

Hi,

The tensor image header information is assumed to match the seed file unless you tell it otherwise. In this case the seed file is of higher resolution and thus contains more voxels than the tensor data. 

The raw format used by Camino doesn't have header information, so it guesses the data dimensions from the seed file unless you tell it otherwise. This can be done by passing a NIFTI header. For example, if you reconstructed the tensor from an image named DWI.nii.gz, you could do

  track -inputmodel dt -seedfile /home/marina/Desktop/fsmask_1mm_resamp2x2x2.nii.gz -curvethresh 60 -inputfile DTI_RAWDATA/difftensor_nomask.Bdouble -outputfile DTI_RAWDATA/traccia.Bfloat -header DWI.nii.gz

This tells track that the DT image has dimensions defined by DWI.nii.gz, and not by fsmask_1mm_resamp2x2x2.nii.gz.


Phil


On Apr 19, 2012, at 6:11 AM, Curci Marina Carmela wrote:

> Hello to everyone!
> 
> I'm new on camino and I'm trying to use the toolkit with my DTI dataset.
> I have some problems during the tractography.
> The mask I'm using it's a mask of the white matter obtained with Freesurfer. Physical dimensions are the same of the file containing the tensor, but resolutions are different.
> When i try to launch track command I have this kind of error:
> 
> 
> track -inputmodel dt -seedfile /home/marina/Desktop/fsmask_1mm_resamp2x2x2.nii.gz -curvethresh 60 -inputfile DTI_RAWDATA/difftensor_nomask.Bdouble -outputfile DTI_RAWDATA/traccia.Bfloat
> 
> Apr 19, 2012 12:09:44 PM apps.StreamlineTractography initVariables
> INFO: Defining input physical space from seed file
> Apr 19, 2012 12:09:46 PM misc.LoggedException logException
> SEVERE: Exception in thread "main" class data.DataSourceException: No more voxels in data source.
> 	at data.VoxelOrderDataSource.readNextVoxel(VoxelOrderDataSource.java:230)
> 	at data.VoxelOrderDataSource.nextVoxel(VoxelOrderDataSource.java:189)
> 	at tractography.DT_TractographyImage.<init>(DT_TractographyImage.java:81)
> 	at tractography.DT_TractographyImage.getDT_TractographyImage(DT_TractographyImage.java:277)
> 	at apps.StreamlineTractography.execute(StreamlineTractography.java:784)
> 	at apps.EntryPoint.main(EntryPoint.java:275)
> 
> I'm not able to find where is the problem. Could you help me please??
> 
> Thank you,
> Marina_______________________________________________
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