One more Question... If I used <--seg-erode 1 > then I will have the mean diffusivity (MD) as an output of mri_segstats
Is that right?
Thanks, Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, June 27, 2014 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Right hemispheric white matter mean FA
I think that would work, but it maybe more effort than needed. You could have just run
mri_segstats --seg /aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i fa.anat.mgh --sum fa.stats
And just look at segmentation 41 (RH WM)
Or you could add --segid 41
and only RH WM will appear in the table
I would also add --seg-erode 2 to reduce the amount of partial voluming with GM
doug
On 06/27/2014 02:28 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
In order to calculate the right hemispheric white matter mean fractional anisotropy (FA), I did the following:
1.I used " rh.dwhite.ribon.mgz" as input in mri_binaraize to create a binary mask (I did convert mgz to nii and vice versa)
2.I used mri_segstats --seg /aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i fa.anat.mgh -mask <MY BINARY MASK_THE OUTPUT OF MY PREVIOUS STEP>--sum fa.stats to generate the statistics .
Is that right?
Kindly, Any suggestions or comments?
Thanks,
Mohamad
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