The mean diffusivity is the same as the apparent diffusion coef (ADC); there should be an adc volume in the output of dt_recon doug
On 07/01/2014 12:38 PM, Alshikho, Mohamad J. wrote:
Thanks Doug, Actually I want to calculate the MD just for the right and left hemispheric white matter. The output of dt_recon doesn't include anything about the mean diffusivity (i.e we have just the eignvals.nii ) so what is the best way to generate the MD as a nifty file? Is it by using fslsplit on eignvals.nii or as I did fslmaths command line to divide eignvals to L1, L2, L3 as I did in my first step or what do you think?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, July 01, 2014 10:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mean diffusuvuty MD
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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