[Camino-users] converting vtk files to nifti

[Philip A Cook]

Hi,

I would start by calling procstreamlines and outputing the heat map of streamline counts as a NIFTI image. That is, you would do:

  # track in some data
  track ... > lines.Bfloat

  # Using FSL nodif_brain_mask.nii.gz for NIFTI header information
  procstreamlines -inputfile lines.Bfloat -outputacm -outputroot acmForFSL_ -header nodif_brain_mask.nii.gz

This will give you a heat map you can view in fslview, but it is in the diffusion space, not the T1 space. You would need to align the DWI to the T1 somehow, and then resample the heat map into the T1 image space. 



> On Nov 1, 2016, at 3:40 PM, Dr. Mohit Saxena <mohitindelhi at yahoo.com> wrote:
> 
> Hi I am new to camino
> I used BedpostX from fsl to perform determininstic tractography
> I could generate and view vtk files but:
> 1. i want to view the T1 file (nifti) in background
> 2. or else is there a way to convert vtk to nifti so i can overlay the tracts onto the fslview
> 
> Any prompt answer would be a great help 
> 
> Thanks
>  
> 
> Thanks & Regards
> 
> Dr. Mohit Saxena
>     (Ph.D Neurology)
> 
> 
> Department of Neurology
> School of Medicine
> University Hospitals
> Case Medical Center
> Case Western Reserve University
> Cleveland Ohio 44106
> 
> 
> _______________________________________________
> Camino-users mailing list
> Camino-users at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/camino-users