[Camino-users] rgbscalarimage

[Philip A Cook]

Hi Michael,

Good meeting you at ISMRM - I'm just replying to update the list

rgbscalarimg is unique amongst Camino programs because it lets you alter the output header type, eg you can input an .nii and output a .mha. This was done because Paraview didn't support RGB nii images at the time (it now does). 

Any time image formats are mixed, there is a potential for misalignment. This is unfortunately still an issue for Paraview, where we often need to display VTK and .nii files and possibly other things together. 

Outputting the same image format as the input should make the output internally consistent, ie it should render in the same place as the input image. But it might still be offset and / or flipped compared to a VTK mesh, streamlines, or an MHA file.



On Apr 19, 2013, at 1:52 AM, Michael Zeineh wrote:

> Hi all,
> 
> I am getting some weird error w/ rgbscalarimg. I want to superimpose my tracks on an FA map using paraview. However, the tracks are not superimposing properly and are shifted by some value.
> 
> I suspect it is rgbscalarimg, which when I run with the following command:
> rgbscalarimg -scalarfile *FA.nii -outputfile fa.mhd -inputfile EIG.Bdouble -rgbgamma 0.0
> 
> Gives me the following error:
> Apr 18, 2013 9:40:25 PM apps.RGB_ScalarImage writeMeta
> WARNING: Header template is not Meta, physical space information may be lost
> 
> I know this is the culprit, because if I zero out the sforms and qforms in my seed files and my FA file, things overlap perfectly (though this is an undesirable hack).
> 
> Any help would be wonderful, thank you. It seems I need some kind of tool to translate nifti headers to mhd/mha headers. c3d does this from the nifti files, but the images are still offset from the tracks generated from the same nifti files.
> 
> Michael Zeineh, M.D.-Ph.D.
> Assistant Professor, Dept of Radiology
> 300 Pasteur Drive, Room S-047
> Stanford, CA  94305-5105
> t:  650-721-1419
> c: 650-722-2235
> f:  650-498-5374
> mzeineh at stanford.edu
> 
> 
> 
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