Hi Stephanie

it depends what you want to compute the mean over.

cheers Bruce On Fri, 18 Jan 2019, Winkelbeiner, Stephanie A wrote:

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Thanks for your answer, Bruce!

I wasn't aware that it extracts data straight from the surface image. I was wondering which image type I would have to specify with mris_anatomical_stats if I wanted to use it to extract FA values from dti_FA.nii.gz.

But since I want the mean FA values, I feel that mri_segstats would be the way to go for these images. Would you agree?

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, January 17, 2019 2:42 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] mris_anatomical_stats input image?

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Hi Stephanie

specifying "pial" directs it to use the ?h.pial surfaces for e.g. surface area measurement. What information are you hoping to extract from the orig.mgz?

cheers Bruce

On Thu, 17 Jan 2019, Winkelbeiner, Stephanie A wrote:

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Hi Freesurfers,

I’m using the below command to extract GM values:

mris_anatomical_stats -mgz \

-cortex label/lh.cortex.label \

-f stats/lh.250.aparc.pial.stats \

-b -a 250.aparc \

-c label/colortable.ctab \

$subject lh pial

Specifying “pial” which image does the command actually use? The mri/orig.mgz?

Thanks for your help!

Stephanie

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