You can use mri_convert aseg.mgz --erode-seg 1 aseg.e1.mgz and visualze aseg.e1.mgz vs aesg.mgz you can use aseg.e1.mgz as input to mri_segstats (and turn off the erode)

On 04/15/2016 11:08 AM, Elijah Mak wrote:

Hi Doug,

I have pasted the previous emails below. I have computed mri_segstats to extract the FA and MD from resampled aparc+aseg.mgz in diffusion space. -seg-erode 1 was performed during mri_segstats. Now, I will like to visually inspect the results of that erosion for the left and right hippocampal structures. Is there anyway I can do that and compare that against the uneroded hippocampus?

I don't think mri_segstats -seg-erode 1 produce any volumetric outputs so I am not sure.

Thanks.

Best Wishes,

Elijah

Douglas N Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Mon, 11 Apr 2016 08:11:06 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160411

You can load it as an overlay in freeview make sure to specify the registration file as that compted for the DTI. Also make sure to set the threshold to something like 0.5 On 04/11/2016 09:41 AM, Elijah Mak wrote: > Hi Freesurfer Community, >

...

I have performed -seg-erode 1 during mri_segstats on resampled >

subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1

...

anatomical space to visually inspect whether PVE has been adequately accounted for? > > Thank you. > > Best Wishes, > Elijah

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