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 mailto:greve@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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