what was your command line?rh.ctx-rh-bankssts.label is not a file name that would have been created by mri_annotation2label (and bankssts is not in the 2005 atlas). Are you sure it was not created by mri_label2label? That can create vertex number with -1 if the volume method is used. doug
On 05/23/2013 11:39 AM, 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 > > -- 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
