[Camino-users] FA image format problem

[Mojdeh Zamyadi]

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