Hi Doug, I tried what you suggested but don't think sure I've got it right. I'm trying to extract thickness for gyri and sulci separately in labels that I have created and saved as an annotation. I began by using mri_surf2surf to convert the thickness and sulc files to mgh - no errors, although trying to load either in tkmedit just brings up a straight, coloured line running ear to ear (not sure if this is what to expect) . I then comverted the annot file to mgh using mri_label2vol - seemed ok (although one of the labels in the annot did not seem to appear in the resulting volume). I then ran mri_segstats and got the following:
mri_segstats --seg annot_vol.mgh --sum ./annot_stats.txt --in 1000001_thickness_conv.mgh --ctab /usr/local/freesurfer-dev20050905/alex_ACC_colour_LUT.txt --mask 1000001_sulc_conv.mgh --masksign pos Loading annot_vol.mgh Loading 1000001_thickness_conv.mgh Loading 1000001_sulc_conv.mgh NOT INVERTING There were 28632 voxels in the mask Segmentation fault Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:33 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the mask and use a threshold of 0 (or close to 0). Note, you might have to convert the thickness and sulc from curv format to mgh (use mri_surf2surf). doug > What it require a lot of work? What would be the odds of somehting like > that happening in the near future? :) > > On another issue, if the .sulc file encodes dinsitguises between sulcal > and gyral regions with positive and negative signs, is it possible to > extract the thickness of sulcal and gyral regions separately? I remember > seeing a posting about this some time ago, bu can't seem to find it again. > > Thanks again. > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > [EMAIL PROTECTED] > > > > -----Original Message----- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Fri 23/12/2005 9:30 AM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Sulcal depth > > not all that easily, although I guess we could write out something from > mris_inflate that has the units of mm. > > On Fri, 23 Dec 2005, Fornito, Alexander wrote: > >> Hi all, >>> From my understanding, ?h.sulc can be used to measure sulcal depth. >> I'm wandering if it is possible to use this to get the depth of a sulcus >> within an ROI, and if so, how you would extract the relevant measures, >> i.e.., would it be obtainable through mris_anatomical_stats? >> Thanks, >> Alex >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> The University of Melbourne >> [EMAIL PROTECTED] >> >> ________________________________ >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
