So, read_label could be used to load the label in, and then that could be used to pull out the relevant vertices from the .thickness and .sulc files? Also, is there a straightforward way of converting the final column in the .sulc file into mm (as in mm sulcal depth)?
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 11:29 AM To: Fornito, Alexander Cc: [email protected] Subject: RE: [Freesurfer] Sulcal depth I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab. On Fri, 23 Dec 2005, Fornito, Alexander wrote: > Famous last words, but seems simple enough. Will give it a try. Would > just like to clarify what the columns represent in curvature files after > converting to ascii: The first volumn is the vertx id. The next three > columns are the xyz co-ords. The rightmost column is the actual > 'curvature value', e.g., in thickness file, it's the thickness associated > with that vertex, in the sulc file, it's the integrated the distnace the > node moves during inflation, etc.. In which case, for extracting sulcal > and gyral regions separately, I'd need to split vertices based on the > sign of the final column in the sulc file. > > Another question: are the xyz coords talairach or native coords? They're > not surface coords are they? I would've thought surface coords would be > in 2D (although I have been known to get it completely wrong form time to > time!). > > 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 10:36 AM > To: Fornito, Alexander > Cc: [email protected] > Subject: RE: [Freesurfer] Sulcal depth > > sure, just sum them separately. Would be easy to do in matlab (we did it > in our PNAS thickness paper) > On Fri, 23 Dec 2005, Fornito, Alexander wrote: > >> 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: [email protected] >> 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 >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> >> > > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
