Hi Don
I think label2label --dilate does a morphological dilation on the
surface, not a new surface. It is also independent of distance - it just
uses topology - so your approach will be better if you truly want a
circle (although of course if the surface is highly curved then the
metric won't be quite right)
cheers
Bruce
On Sat, 13 Feb 2016, Krieger, Donald N. wrote:
Hi Martha,
A brute force but simple way to do this is to use the list of labels
contained in subjects/nnn/label/lh.cortex and rh.cortex.
Given a vertex x,y,z, go through the file and select the lines for which the
distance to x,y,z <= 2 mm. This will give you a bunch of labels for points
within a circle with 2 mm radius about x,y,z. And all of them will be on
the “white” surface. If your vertex is on a different surface, e.g. pia, or
you want a different geometry, e.g. square, there’s likely a simple variant
which will work.
In my experience mri_label2label –dilate takes a lot of time and I’m not
sure you can restrict it to give you points on the surface that you want. I
think it gives you a new surface which is displaced by a fixed distance from
the one where you start.
I hope this is helpful.
Best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martha Shiell
Sent: Saturday, February 13, 2016 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer tool to automatically generate label
surrounding a given vertex?
Hello Freesurfer community,
I am looking for a way to automatically generate a surface label file of a
specific dimension (e.g. a circle with a specific diameter, or a square),
given a specific vertex and some measure of the desired size.
I have considered to do so by starting with a label file consisting of a
single vertex, and then expanding this label with the mri_label2label tool,
using the --dilate option. I wanted to know though if anyone has any better
suggestions.
Thank you,
Martha
--
Martha M. Shiell, PhD
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
