Hi Danielle,

I think you're doing right. MD value is actually the ADC value, just different names. For RD value, you have to use fslmaths to calculate it from dti_L2 and dti_L3.

e.g.: fslmaths dti_L2 -add dti_L3 -div 2 dti_RD.nii.gz -odt float

Hope this helps : )

Guangyu

On Tue, May 24, 2016 at 11:21 AM, Danielle de Sá Boasquevisque <[log in to unmask]> wrote:

Hi all,
I am starting FSL analyses and preprocessing.
I have stroke patients to extract the mean FA, MD, RD and AD values and I choose a template from Juelich Atlas ( Corticospinal template) to extract those values.
I am not sure if what I am doing is right. So, I got this template and I binarize this mask and convert this using a Mattrix ( standardtodiff.xfms)
So I am using the fslstats command where I write
fslstats dti_FA.nii.gz -k regflirt_stardand2diff_CSTrightmask.nii.gz -M -S ( for the right corticospinal mask) 

For the MD value, I substitute the dti_FA.nii.gz for the dti_MD.nii.gz
For de AD value, I mean that I have to use the dti_L1
For RD value and ADC value I don`t know how to do.

I don`t no if I am correct with fslstats or maybe I am wrong with these concepts.

Tks for help
Danielle