>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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422