Another way to do this is to use mri_volsynth to create a surface overlay with a single vertex 1 and everything else 0, then use mri_surf2surf to smooth the overlay to create a disk on the surface, then use mri_binarize, then use mri_vol2label to create a surface label. for mri_volsynth, use --pdf delta --pdf-crsf vertexno 0 0 0 --dim nvertices 1 1 1 for mri_vol2label use the --surf option you can run both with --help to get more info
On 02/13/2016 02:41 PM, Krieger, Donald N. wrote: > Yes, thanks ... from my notes: > This command contracts the selected surface vectors 3.0 mm > and places the resultant new surface file in surf/lh.white-3: > mris_expand lh.white -3.0 lh.white-3 > > Best regards, > > Don >> -----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 2:37 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Freesurfer tool to automatically generate label >> surrounding a given vertex? >> >> mris_expand probably >> On Sat, 13 Feb 2016, Krieger, Donald N. wrote: >> >>> 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 >>> >>> >>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
