Thanks for posting back about this, Bruce. I am thinking about a different function which probably is not called --dilate. One specifies a surface, e.g. white, and gets back a new surface displaced by the distance you specify whose tangent is parallel to the tangent of the starting surface at the nearest point.
> -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Saturday, February 13, 2016 1:44 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Freesurfer tool to automatically generate label > surrounding a given vertex? > > 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.
