[Camino-users] FA and MD alignment, registration of Freesurfer labels

[Philip A Cook]

Hi,

If you created the nii for FA and the MD with the same reference header, they ought to produce the same output. Can you send me the commands you ran? You can also run

  niftiheader -readheader <image>

to get a printout of the header information for the images involved. 

The Paraview problem is a longstanding issue with inconsistency between VTK and NIfTI data in that software. In general a Nifti image loaded into Paraview won't overlap with the same image in VTK format. I should at least make note of this in the tutorial. I would like to find a fix but I think there are heuristics inside the Paraview NIFTI code to determine how to orient things, so I've not found a single transformation that has worked consistently. 

On Jul 29, 2014, at 9:14 AM, Oren Geri <oren_geri at yahoo.com> wrote:

> Hi,
> I have a few questions about creating connectivity matrix with Camino and Freesurfer labels.
>  
> First, I followed the tutorial instructions to create fa.nii and md.nii files.
> I checked these files using SPM8 display command. The images didn't seem to be aligned, also I got different "Origin" and "Dir Cos" values for the images and a warning : "shears involved" message (This problem doesn’t occur using the tutorial data).
>  
> Second, I used Freesurfer for labeling different volumes and SPM to register the labels file "aprac+aseg.nii" using "orig.nii" (the structural file) as source and the B0 data as reference.
> I viewed some of the streamlines created by Camino (following the tutorial using dtfit) and volumes from the registered image of labels with Paraview. It seems that there is a registration problem since the streamlines appear shifted from the place they should be.
> Thanks a lot,
>  Oren
> 
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