I don't know about the first step but 2 and 3 look ok. But why are you using the aseg? It will just give you the lh and rh cerebral WM
On 06/30/2014 03:11 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
In order to calculate the mean diffusivity MD in my DTI data I did the following:
1.For the Eigvals.nii (the output of dt_recon) I used the following command line: fslmaths eigvals –div 3 md.nii
2.mri_vol2vol –mov md.nii --reg register.dat --fstarg -- interp nearest -- o md.anat.mgh
3.mri_segstats --seg $SUBJECTS_DIR/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --seg-erode 2 --i md.anat.mgh --sum md.stats
is this correct ?
I highly appreciate any suggestions and advices
Mohamad
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