sorry, it fell through the cracks. Please feel free to resend if I don't get back in a reasonable amount of time... Try this command instead
mri_segstats --annot subjectname lh aparc --sum lh.sulc.sum --i surf/lh.sulc the output will be lh.sulc.sum doug On 08/16/2012 07:02 PM, Hugh Pemberton wrote: > Hi Doug, did you get a chance to see my last e mail by the way? The > one below. > Thanks very much indeed, > Hugh > > On 15 August 2012 10:32, Hugh Pemberton <[email protected] > <mailto:[email protected]>> wrote: > > 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 > <[email protected] <mailto:[email protected]>> 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 <[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> > > Subject: Re: [Freesurfer] (no subject) > To: [email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > Message-ID: <[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>> > > 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 > [email protected] <mailto:[email protected]> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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 . 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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
