Great, thanks.
On another issue, I've noticed that using mris_convert to convert ?h.area to ascii produces the same area values in the resulting file, irrepsective of whether pial or white surfaces are specified in the command. This contrasts mris_anatomical_stats, which gives different values. Is it possible to extract pial and white surface area separately for sulcal and gyral regions? Thanks again, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/01/2006 12:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] .sulc in tksurfer
yes, that makes sense. On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi Bruce, I'm trying to extract thickness for sulci and gyri separately. From what I understand, positive .sulc values suggest sulci and negative .sulc values suggest gyri. I'd like to play around with this distinction (e.g., call everything with a .sulc value < .35 'gyral'), and am wandering if adjusting the midpoint in tksurfer allows me to precisly visualize what changing this threshold does. Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy with in tksurfer, say .35, than go back and split the .thickness file into vertices with .sulc values above and below .35, knowing that this distinction between sulcal and gyral will correspond to the one shown by the colour display I visualized in tksurfer.
I'm pretty sure the values in the tksurfer threshold midpoint scale correspond to those in the curvature file, since they seem to change depednig on the curvature file loaded (e.g., the range for .sulc files is different to the range for .thickness files). Just want to double-check. Hope this makes sense, Alex
the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors)
On Wed, 4 Jan 2006, Fornito, Alexander wrote:
Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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