HI Doug,

I tried the mris_anatomical_stats and may well be doing it wrong but got this as the result:

hughp@naoshi-WS:~/freesurfer/subjects$ mris_anatomical_stats -a ABM/surf/lh.sulc -b ABM lh computing statistics for each annotation in ABM/surf/lh.sulc. reading volume /home/hughp/freesurfer/subjects/ABM/mri/wm.mgz... reading input surface /home/hughp/freesurfer/subjects/ABM/surf/lh.white... reading input pial surface /home/hughp/freesurfer/subjects/ABM/surf/lh.pial... reading input white surface /home/hughp/freesurfer/subjects/ABM/surf/lh.white... CTABfindAnnotation: ct was NULL No such file or directory Segmentation fault (core dumped)

Not sure how to rectify this, any ideas?

Many thanks again, Hugh

On 15 August 2012 01:42, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

Hi Hugh, you can run mris_anatomical_stats passing it the sulc file as input. This will give you averages within aparc. I'm not sure what you mean by "measuring cortical folding". What measure would you accept? There's the sulcal depth and then there's curvature (?h.curv). There are two types of "normalization". One is intensity normalization which is a preprocessing step before the segmentation. "Normalization" is also refers to intersubject registration. Probably you mean the latter. doug

On 08/13/2012 09:56 PM, Hugh Pemberton wrote:

...

Hi Doug,

Thanks so much for getting back to my original question (have included below) and apologies if my question seems trivial but I'm a bit of a novice with freesurfer.. I've found the ?h.sulc file but how do I go about extracting the sulcal depth measurements? Is there a command like aparcsstats2table?

Also, is there a way of measuring cortical folding with freesurfer? And I've read about the noramlization step but am still not completely clear on it, is this part of the segmentation of white/gray surface and pial surface?

Thanks so much for your help, Best, Hugh

Message: 5 Date: Sun, 12 Aug 2012 22:25:02 -0400 From: Douglas Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>

Subject: Re: [Freesurfer] (no subject) To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.** harvard.edu freesurfer@nmr.mgh.harvard.edu> Message-ID: <5028657E.8070908@nmr.mgh.**harvard.edu5028657E.8070908@nmr.mgh.harvard.edu<mailto: 5028657E.8070908@nmr.**mgh.harvard.edu5028657E.8070908@nmr.mgh.harvard.edu

...

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Content-Type: text/plain; charset="iso-8859-1"

The values are in the ?h.sulc file doug

On 8/12/12 10:12 PM, Hugh Pemberton wrote:

...

Hi,

How can I get sulcal depth measurements from Freesurfer?

Cheers, Hugh

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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