[Camino-users] FA image format problem

[Philip A Cook]

Try

cat dt.Bdouble | fa -header someheader.nii.gz -outputfile fa.nii.gz

where someheader.nii.gz contains the relevant header information

On Aug 13, 2013, at 2:51 PM, Mojdeh Zamyadi wrote:

> Hi all,
> 
> I have a question about the format of the FA image created in camino? I use the following command to make a header file:
> 
> analyzeheader -datadims $dim1 $dim2 $dim3 -voxeldims $pixdim1 $pixdim2 $pixdim3 -datatype double -outputfile FA.hdr
> 
> (and "fa <DiffTensor.Bdouble > FA.img"  to create the .img file)
> 
> my problem is when I use FSL and try to convert this file into .nii.gz and then open the file in mricron I get the error: "matrix appears bogus", I can ignore this message and the FA.nii.gz file will open but then I'll have problems with overlaying other images on the FA image. In particular, I use itk-snap to segment Thalamus on the FA.img/hdr (created using camino commands), I'll then save the segmentation in .nii in itk-sanp (I've tried the ANALYZE format in itk-sanp but I have the same issues, plus I asked the itk-snap people and they said the nifti format is much more reliabe!). Then I convert FA.img to FA.nii.gz using fslchfiletype and that's when I have the overlaying problems! It seems to me that there is a problem with the way I'm creating the FA.img/hdr pair using camino. Is there a way to directly create .nii.gz FA images?
> 
> Thanks,
> -Mojdeh
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