Doug can you answer this? The vertex indices can be fixed with matlab but more importantly I need to know why there is a slight offset in vertex coordinates.
Thank you! Tina Jeon -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 23, 2013 10:57 AM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with alignment of labeling files generated from the rh.area file hmmm, then I would have thought that they would have vertex indices >=0. Maybe Doug knows? On Thu, 23 May 2013, Tina Jeon wrote: > I generated the labeling file from the corresponding numbers in base file. > The ctx-rh-bankssts was generated from mris_annotation2label with input > -a2005. This is the file with -1 vertex numbers. > > In theory these files should be the same. > > On May 23, 2013, at 10:28 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > wrote: > >> Hi Tina >> >> how did you create it? If the vertex indices are -1 it means they are not >> assigned, and when you load it into tksurfer it will sample them onto the >> surface. You can then save it it will write the new vertex numbers into the >> label file. >> >> Not sure about the offset though. >> Bruce >> >> On Thu, 23 May 2013, Tina Jeon wrote: >> >>> Hello Freesurfers, >>> >>> I have created labeling files from a subject using the area file >>> (previously named base). The label file corresponds to the >>> freesurfer generated cortical label, ctx-rh-bankssts, which I have >>> attached in this email. The labeling files should be the same, >>> however, there are some discrepancies in the files: >>> 1). There is a slight offset in the vertices. >>> 2). A reduced number of vertices in the .label file created from the >>> area file. >>> 3). The vertex numbers are numbered -1. >>> >>> Our goal is to overlay a custom atlas onto a cortical surface >>> generated from amira in freesurfer. Can you please tell how to >>> transform the labeling files so that I can successfully overlay them? >>> >>> I have attached all three files for you. rh.rh_label_2001.label is >>> the labeling file created from the base file, >>> rh.ctx-rh-bankssts.label is the label from freesurfer and the >>> rh.base file I have sent to Bruce the file is too large. When I >>> overlay the rh.rh_label_2001.label and other labels generated from the base >>> file, only parts of the temporal lobe are overlayed. >>> >>> Thank you in advance, >>> >>> Tina Jeon >>> UT Southwestern Medical Center '14 >>> >>> ____________________________________________________________________ >>> ________ >>> UT Southwestern Medical Center >>> The future of medicine, today. >>> >> >> >> 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
