Hi,
dti_L1 and dti_L2 are not standard images, but are in individual diffusion
space.
You can either use normalized images of L1 and L2 (like those in the
merged file all_L1_skeletonised) or transform your mask in diffusion
space.
best,
Angela
> Hi everyone,
>
> I need to extract the average radial diffusivity and the average axial
> diffusivity in a certain ROI, for each of my subjects. I therefore used
> fslmaths dti_L1 AD
> fslmaths dti_L2 -add dti_L3 -div 2 RD
> to compute the AD and RD images for each subject, and then
> fslstats AD.nii.gz -k mask.nii.gz -M
> fslstats RD.nii.gz -k mask.nii.gz -M
> to compute the average AD/RD in my region of interest. However, fslstats
> gives an error, because apparently the mask that I have for my ROI,
> created from the 2mm MNI standard, is of a (slightly) different size from
> that of the AD/RD image. The resolution also seems to be slightly
> different (1.97917x1.97917x2 mm for AD/RD and 2x2x2 mm for the mask).
>
> My question is, therefore: should the mask somehow be
> transformed/registered to the AD/RD image, or should I recreate the mask
> using the AD/RD image as a template? Many thanks in advance for any help!
>
> Tudor
>
>
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