Hi Tina, I don't really understand what you mean by offset. Do you mean when you visualize on the surface? The placement is completely dictated by the index you assign in that case. If you are doing this in matlab, make sure you account for the fact that the vertex numbers are 0 based not 1-based doug
On 05/24/2013 11:12 AM, Tina Jeon wrote: > 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 > > -- 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
