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.
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.
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.
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.
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" 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.
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
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" 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.
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.
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:fischl@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" 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.
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.
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:fischl@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" 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.
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.
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