From --help on mri_label2vol:
--proj type start stop delta
Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface.
Not sure why it's splotchy. Can you lower the delta?
doug
Fornito, Alexander wrote:
I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) 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
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol
This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does:
set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz)doug
On Sat, 3 Dec 2005, Fornito, Alexander wrote:
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac "means that start, stop, and delta are relative to the thickness at each vertex." I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? 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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