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 <gr...@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 <gr...@nmr.mgh.harvard.edu <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> Subject: Re: [Freesurfer] (no subject) >> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu <freesurfer@nmr.mgh.harvard.edu>> >> Message-ID: >> <5028657e.8070...@nmr.mgh.**harvard.edu<5028657e.8070...@nmr.mgh.harvard.edu><mailto: >> 5028657E.8070908@nmr.**mgh.harvard.edu<5028657e.8070...@nmr.mgh.harvard.edu> >> >> >> >> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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