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 alexander.fornito@wh.org.au
-----Original Message----- From: greve@nmr.mgh.harvard.edu [mailto:greve@nmr.mgh.harvard.edu] 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 alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] 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 alexander.fornito@wh.org.au
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