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" fischl@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.
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