Without -th3, it will compute cortical volume using thickness*surface area. With -th3 it computes volume using truncated tetrahedra. -th3 will become the default in v6 (requiring -no-th3 to revert back to thickness*area)

On 3/14/16 10:49 AM, Kaiming Yin wrote:
Dear Douglas,

I saw the previous tutorials didn't include this "-th3" flag, is there any difference between the following two command lines?

mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject1 lh white

mris_anatomical_stats        -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject1 lh white


Thanks,
Kaiming


---------- Forwarded message ----------
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Cc: 
Date: Mon, 7 Mar 2016 18:50:01 -0500
Subject: Re: [Freesurfer] mris_anatomical_stats -th3
/*!
  \fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
  \brief Compute vertex-wise volume based on dividing each obliquely truncated
  trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's
  srf2vol matlab script.
  \params w is white surface, p is pial. Output is an MRI struct of size nvertices
 */



On Sun, Mar 6, 2016 at 7:53 PM, Kaiming Yin <yinkaiming6987@gmail.com> wrote:
Dear guys,

I checked one of my subjects file /stats/lh.aparc.stats, in which it said the commandline as:

mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject1 lh white

what does the flag "-th3" mean? I'm using Freesurfer v6.0 beta.

Thanks,
Kaiming