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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