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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