Hi,
You should have one transformation between your structural and diffusion spaces. This can be derived from registering the FA or the b=0 or another diffusion image (as long as it contains sufficient detail and structure) to the T1-weighted structural image. Once you have done this registration once, then you don't need to do it again for other images in the diffusion space. You can transform your mask from the structural to the diffusion space just once and then use it for FA, RD, MD, or any other image in the diffusion space.
I hope this helps.
All the best,
Mark
On 31 Jul 2014, at 08:31, M. alshikho <[log in to unmask]> wrote:
> Hi FSL Experts.
> What is the best way in FSL to estimate the right or left hemispheric white matter?
> I used a mask for the right hemispheric white matter from the T1 segmentation in Freesurfer then I registered this mask to FA map using FLIRT then I used the following command line : fslstats -i dti_FA.nii.gz -k <the registered mask to FA map> -V
>
> Is this correct? what if I registered my mask to MD map or RD map then I will have a different volume!
>
> Any suggestions please?
>
> Best regards,
> Mohamad
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