Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
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Thank you.
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
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Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you.
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hello,
I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface?
Thanks, Anna
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hello, > > I am trying to create a new surface area on the inflated brain given by freesurfer > using recon-all. I make to create my own ROI that is co-registered onto this surfer. > Ultimately, I want to be able to take information from a different data source such as > EEG and have it co-registered onto the inflated surface. How do I go about creating > this new ROI surface? > > Thanks, > Anna > > =================================== > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World > Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing > of our services, staff and locations. Confidentiality Note: This message is intended > for use only by the individual or entity to which it is addressed and may contain > information that is privileged, confidential, and exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient or the > employee or agent responsible for delivering the message to the intended recipient, you > are hereby notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this communication in error, > please contact the sender immediately and destroy the material in its entirety, whether > electronic or hard copy. Thank you. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
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Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI?
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 10:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hello, > > I am trying to create a new surface area on the inflated brain given by freesurfer > using recon-all. I make to create my own ROI that is co-registered onto this surfer. > Ultimately, I want to be able to take information from a different data source such as > EEG and have it co-registered onto the inflated surface. How do I go about creating > this new ROI surface? > > Thanks, > Anna > > =================================== > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World > Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing > of our services, staff and locations. Confidentiality Note: This message is intended > for use only by the individual or entity to which it is addressed and may contain > information that is privileged, confidential, and exempt from disclosure under > applicable law. If the reader of this message is not the intended recipient or the > employee or agent responsible for delivering the message to the intended recipient, you > are hereby notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this communication in error, > please contact the sender immediately and destroy the material in its entirety, whether > electronic or hard copy. Thank you. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi, > > I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? > > Thanks, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 10:44 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > I'm not exactly sure what you mean, but if you register EEG electrodes to > the white or pial surface, then you can visualize them on the inflated > surface trivially. That is, you can create your ROI on any surface of the > same hemisphere/subject and visualize it on any other > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna > wrote: > >> Hello, >> >> I am trying to create a new surface area on the inflated brain given by freesurfer >> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >> Ultimately, I want to be able to take information from a different data source such as >> EEG and have it co-registered onto the inflated surface. How do I go about creating >> this new ROI surface? >> >> Thanks, >> Anna >> >> =================================== >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >> of our services, staff and locations. Confidentiality Note: This message is intended >> for use only by the individual or entity to which it is addressed and may contain >> information that is privileged, confidential, and exempt from disclosure under >> applicable law. If the reader of this message is not the intended recipient or the >> employee or agent responsible for delivering the message to the intended recipient, you >> are hereby notified that any dissemination, distribution or copying of this >> communication is strictly prohibited. If you have received this communication in error, >> please contact the sender immediately and destroy the material in its entirety, whether >> electronic or hard copy. Thank you. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
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Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label.
Thank you, Anna ________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi, > > I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? > > Thanks, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 10:44 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > I'm not exactly sure what you mean, but if you register EEG electrodes to > the white or pial surface, then you can visualize them on the inflated > surface trivially. That is, you can create your ROI on any surface of the > same hemisphere/subject and visualize it on any other > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna > wrote: > >> Hello, >> >> I am trying to create a new surface area on the inflated brain given by freesurfer >> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >> Ultimately, I want to be able to take information from a different data source such as >> EEG and have it co-registered onto the inflated surface. How do I go about creating >> this new ROI surface? >> >> Thanks, >> Anna >> >> =================================== >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >> of our services, staff and locations. Confidentiality Note: This message is intended >> for use only by the individual or entity to which it is addressed and may contain >> information that is privileged, confidential, and exempt from disclosure under >> applicable law. If the reader of this message is not the intended recipient or the >> employee or agent responsible for delivering the message to the intended recipient, you >> are hereby notified that any dissemination, distribution or copying of this >> communication is strictly prohibited. If you have received this communication in error, >> please contact the sender immediately and destroy the material in its entirety, whether >> electronic or hard copy. Thank you. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Thank you.
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. > > Thank you, > Anna > ________________________________________ > > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 1:16 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > can you explain what the ROI is supposed to represent? If you can create > it in the volume, you can use mri_vol2surf to map it onto the surface. > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >> >> Thanks, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 10:44 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> I'm not exactly sure what you mean, but if you register EEG electrodes to >> the white or pial surface, then you can visualize them on the inflated >> surface trivially. That is, you can create your ROI on any surface of the >> same hemisphere/subject and visualize it on any other >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna >> wrote: >> >>> Hello, >>> >>> I am trying to create a new surface area on the inflated brain given by freesurfer >>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>> Ultimately, I want to be able to take information from a different data source such as >>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>> this new ROI surface? >>> >>> Thanks, >>> Anna >>> >>> =================================== >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>> of our services, staff and locations. Confidentiality Note: This message is intended >>> for use only by the individual or entity to which it is addressed and may contain >>> information that is privileged, confidential, and exempt from disclosure under >>> applicable law. If the reader of this message is not the intended recipient or the >>> employee or agent responsible for delivering the message to the intended recipient, you >>> are hereby notified that any dissemination, distribution or copying of this >>> communication is strictly prohibited. If you have received this communication in error, >>> please contact the sender immediately and destroy the material in its entirety, whether >>> electronic or hard copy. Thank you. >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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Thank you.
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
To create the volume ROI, I found something that said to use:
scuba -v $filename
to then make a new ROI.
I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 1:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
yes, create a volume ROI and you can map it onto the surface using mri_vol2surf
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. > > Thank you, > Anna > ________________________________________ > > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 1:16 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > can you explain what the ROI is supposed to represent? If you can create > it in the volume, you can use mri_vol2surf to map it onto the surface. > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >> >> Thanks, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 10:44 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> I'm not exactly sure what you mean, but if you register EEG electrodes to >> the white or pial surface, then you can visualize them on the inflated >> surface trivially. That is, you can create your ROI on any surface of the >> same hemisphere/subject and visualize it on any other >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna >> wrote: >> >>> Hello, >>> >>> I am trying to create a new surface area on the inflated brain given by freesurfer >>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>> Ultimately, I want to be able to take information from a different data source such as >>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>> this new ROI surface? >>> >>> Thanks, >>> Anna >>> >>> =================================== >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>> of our services, staff and locations. Confidentiality Note: This message is intended >>> for use only by the individual or entity to which it is addressed and may contain >>> information that is privileged, confidential, and exempt from disclosure under >>> applicable law. If the reader of this message is not the intended recipient or the >>> employee or agent responsible for delivering the message to the intended recipient, you >>> are hereby notified that any dissemination, distribution or copying of this >>> communication is strictly prohibited. If you have received this communication in error, >>> please contact the sender immediately and destroy the material in its entirety, whether >>> electronic or hard copy. Thank you. >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. 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Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
> To create the volume ROI, I found something that said to use: > > scuba -v $filename > > to then make a new ROI. > > I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? > > Thank you, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 1:52 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > yes, create a volume ROI and you can map it onto the surface using > mri_vol2surf > > cheers > Bruce > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >> >> Thank you, >> Anna >> ________________________________________ >> >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:16 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> can you explain what the ROI is supposed to represent? If you can create >> it in the volume, you can use mri_vol2surf to map it onto the surface. >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>> >>> Thanks, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 10:44 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>> the white or pial surface, then you can visualize them on the inflated >>> surface trivially. That is, you can create your ROI on any surface of the >>> same hemisphere/subject and visualize it on any other >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna >>> wrote: >>> >>>> Hello, >>>> >>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>> Ultimately, I want to be able to take information from a different data source such as >>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>> this new ROI surface? >>>> >>>> Thanks, >>>> Anna >>>> >>>> =================================== >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>> for use only by the individual or entity to which it is addressed and may contain >>>> information that is privileged, confidential, and exempt from disclosure under >>>> applicable law. If the reader of this message is not the intended recipient or the >>>> employee or agent responsible for delivering the message to the intended recipient, you >>>> are hereby notified that any dissemination, distribution or copying of this >>>> communication is strictly prohibited. If you have received this communication in error, >>>> please contact the sender immediately and destroy the material in its entirety, whether >>>> electronic or hard copy. Thank you. >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> 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. >>> >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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Thank you.
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Thank you.
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Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
Hi,
i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this?
I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following:
mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz
among other similar variations. Am I just inputting it wrong or am I just missing information?
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote:
> To create the volume ROI, I found something that said to use: > > scuba -v $filename > > to then make a new ROI. > > I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? > > Thank you, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 1:52 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > yes, create a volume ROI and you can map it onto the surface using > mri_vol2surf > > cheers > Bruce > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >> >> Thank you, >> Anna >> ________________________________________ >> >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:16 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> can you explain what the ROI is supposed to represent? If you can create >> it in the volume, you can use mri_vol2surf to map it onto the surface. >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>> >>> Thanks, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 10:44 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>> the white or pial surface, then you can visualize them on the inflated >>> surface trivially. That is, you can create your ROI on any surface of the >>> same hemisphere/subject and visualize it on any other >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna >>> wrote: >>> >>>> Hello, >>>> >>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>> Ultimately, I want to be able to take information from a different data source such as >>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>> this new ROI surface? >>>> >>>> Thanks, >>>> Anna >>>> >>>> =================================== >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>> for use only by the individual or entity to which it is addressed and may contain >>>> information that is privileged, confidential, and exempt from disclosure under >>>> applicable law. If the reader of this message is not the intended recipient or the >>>> employee or agent responsible for delivering the message to the intended recipient, you >>>> are hereby notified that any dissemination, distribution or copying of this >>>> communication is strictly prohibited. If you have received this communication in error, >>>> please contact the sender immediately and destroy the material in its entirety, whether >>>> electronic or hard copy. Thank you. >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> 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. >>> >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi, > > i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? > > I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: > > mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz > > among other similar variations. Am I just inputting it wrong or am I just missing information? > > Thank you, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 4:23 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > scuba is very old and deprecated. Try using freeview instead > > cheers > Bruce > On Mon, 26 Sep > 2016, Crawford, Anna wrote: > >> To create the volume ROI, I found something that said to use: >> >> scuba -v $filename >> >> to then make a new ROI. >> >> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >> >> Thank you, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:52 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> yes, create a volume ROI and you can map it onto the surface using >> mri_vol2surf >> >> cheers >> Bruce >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:16 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> can you explain what the ROI is supposed to represent? If you can create >>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>> >>>> Thanks, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 10:44 AM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>> the white or pial surface, then you can visualize them on the inflated >>>> surface trivially. That is, you can create your ROI on any surface of the >>>> same hemisphere/subject and visualize it on any other >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Sep 2016, Crawford, Anna >>>> wrote: >>>> >>>>> Hello, >>>>> >>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>> Ultimately, I want to be able to take information from a different data source such as >>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>> this new ROI surface? >>>>> >>>>> Thanks, >>>>> Anna >>>>> >>>>> =================================== >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>> for use only by the individual or entity to which it is addressed and may contain >>>>> information that is privileged, confidential, and exempt from disclosure under >>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>> are hereby notified that any dissemination, distribution or copying of this >>>>> communication is strictly prohibited. If you have received this communication in error, >>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>> electronic or hard copy. Thank you. >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> 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. >>>> >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
Hi,
I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna
mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 26, 2016 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi, > > i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? > > I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: > > mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz > > among other similar variations. Am I just inputting it wrong or am I just missing information? > > Thank you, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 4:23 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > scuba is very old and deprecated. Try using freeview instead > > cheers > Bruce > On Mon, 26 Sep > 2016, Crawford, Anna wrote: > >> To create the volume ROI, I found something that said to use: >> >> scuba -v $filename >> >> to then make a new ROI. >> >> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >> >> Thank you, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:52 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> yes, create a volume ROI and you can map it onto the surface using >> mri_vol2surf >> >> cheers >> Bruce >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:16 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> can you explain what the ROI is supposed to represent? If you can create >>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>> >>>> Thanks, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 10:44 AM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>> the white or pial surface, then you can visualize them on the inflated >>>> surface trivially. That is, you can create your ROI on any surface of the >>>> same hemisphere/subject and visualize it on any other >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Sep 2016, Crawford, Anna >>>> wrote: >>>> >>>>> Hello, >>>>> >>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>> Ultimately, I want to be able to take information from a different data source such as >>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>> this new ROI surface? >>>>> >>>>> Thanks, >>>>> Anna >>>>> >>>>> =================================== >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>> for use only by the individual or entity to which it is addressed and may contain >>>>> information that is privileged, confidential, and exempt from disclosure under >>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>> are hereby notified that any dissemination, distribution or copying of this >>>>> communication is strictly prohibited. If you have received this communication in error, >>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>> electronic or hard copy. Thank you. >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> 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. >>>> >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote: > Hi, > > I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? > > Thank you, > Anna > > > mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume > > srclabel = Testing.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label > FREESURFER_HOME /tools/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file Testing.label > No such file or directory > ERROR reading Testing.label > > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 6:20 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > freeview now checks (in the dev version I believe) if the label has been > sampled onto the surface and won't crash, but you need to use > mri_label2label to sample it onto the surface before loading it onto the > inflated surface in freeview > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >> >> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >> >> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >> >> among other similar variations. Am I just inputting it wrong or am I just missing information? >> >> Thank you, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 4:23 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> scuba is very old and deprecated. Try using freeview instead >> >> cheers >> Bruce >> On Mon, 26 Sep >> 2016, Crawford, Anna wrote: >> >>> To create the volume ROI, I found something that said to use: >>> >>> scuba -v $filename >>> >>> to then make a new ROI. >>> >>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:52 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> yes, create a volume ROI and you can map it onto the surface using >>> mri_vol2surf >>> >>> cheers >>> Bruce >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 1:16 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> can you explain what the ROI is supposed to represent? If you can create >>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>> >>>>> Hi, >>>>> >>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>> >>>>> Thanks, >>>>> Anna >>>>> ________________________________________ >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> Hi Anna >>>>> >>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>> the white or pial surface, then you can visualize them on the inflated >>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>> same hemisphere/subject and visualize it on any other >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>> wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>> this new ROI surface? >>>>>> >>>>>> Thanks, >>>>>> Anna >>>>>> >>>>>> =================================== >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>> electronic or hard copy. Thank you. >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> 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. >>>>> >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote:
I also tried doing setenv SUBJECTS_DIR <path> but that did not work either.
bash: setenv: command not found
Thanks, Anna ________________________________________ From: Crawford, Anna Sent: Tuesday, September 27, 2016 11:12 AM To: Freesurfer support list Subject: RE: [Freesurfer] Co-registering different source data
If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located.
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 27, 2016 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote: > Hi, > > I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? > > Thank you, > Anna > > > mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume > > srclabel = Testing.label > srcsubject = segfs > trgsubject = segfs > trglabel = Testing1N.label > regmethod = volume > > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label > FREESURFER_HOME /tools/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file Testing.label > No such file or directory > ERROR reading Testing.label > > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 6:20 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > freeview now checks (in the dev version I believe) if the label has been > sampled onto the surface and won't crash, but you need to use > mri_label2label to sample it onto the surface before loading it onto the > inflated surface in freeview > > cheers > Bruce > > > On Mon, 26 Sep 2016, Crawford, Anna wrote: > >> Hi, >> >> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >> >> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >> >> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >> >> among other similar variations. Am I just inputting it wrong or am I just missing information? >> >> Thank you, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 4:23 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> scuba is very old and deprecated. Try using freeview instead >> >> cheers >> Bruce >> On Mon, 26 Sep >> 2016, Crawford, Anna wrote: >> >>> To create the volume ROI, I found something that said to use: >>> >>> scuba -v $filename >>> >>> to then make a new ROI. >>> >>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:52 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> yes, create a volume ROI and you can map it onto the surface using >>> mri_vol2surf >>> >>> cheers >>> Bruce >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 1:16 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> can you explain what the ROI is supposed to represent? If you can create >>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>> >>>>> Hi, >>>>> >>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>> >>>>> Thanks, >>>>> Anna >>>>> ________________________________________ >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> Hi Anna >>>>> >>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>> the white or pial surface, then you can visualize them on the inflated >>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>> same hemisphere/subject and visualize it on any other >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>> wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>> this new ROI surface? >>>>>> >>>>>> Thanks, >>>>>> Anna >>>>>> >>>>>> =================================== >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>> electronic or hard copy. Thank you. >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> 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. >>>>> >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote:
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote: > I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. > > bash: setenv: command not found > > Thanks, > Anna > ________________________________________ > From: Crawford, Anna > Sent: Tuesday, September 27, 2016 11:12 AM > To: Freesurfer support list > Subject: RE: [Freesurfer] Co-registering different source data > > If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. > > Thanks, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] > Sent: Tuesday, September 27, 2016 10:50 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Co-registering different source data > > Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that > is already set properly, then do not use the --sd. > > > On 9/27/16 9:38 AM, Crawford, Anna wrote: >> Hi, >> >> I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? >> >> Thank you, >> Anna >> >> >> mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume >> >> srclabel = Testing.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> No such file or directory >> mri_label2label: could not open label file Testing.label >> No such file or directory >> ERROR reading Testing.label >> >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 6:20 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> freeview now checks (in the dev version I believe) if the label has been >> sampled onto the surface and won't crash, but you need to use >> mri_label2label to sample it onto the surface before loading it onto the >> inflated surface in freeview >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >>> >>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >>> >>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>> >>> among other similar variations. Am I just inputting it wrong or am I just missing information? >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 4:23 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> scuba is very old and deprecated. Try using freeview instead >>> >>> cheers >>> Bruce >>> On Mon, 26 Sep >>> 2016, Crawford, Anna wrote: >>> >>>> To create the volume ROI, I found something that said to use: >>>> >>>> scuba -v $filename >>>> >>>> to then make a new ROI. >>>> >>>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 1:52 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> yes, create a volume ROI and you can map it onto the surface using >>>> mri_vol2surf >>>> >>>> cheers >>>> Bruce >>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>> >>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>>> >>>>> Thank you, >>>>> Anna >>>>> ________________________________________ >>>>> >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 1:16 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> can you explain what the ROI is supposed to represent? If you can create >>>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>>> >>>>>> Thanks, >>>>>> Anna >>>>>> ________________________________________ >>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>> >>>>>> Hi Anna >>>>>> >>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>>> the white or pial surface, then you can visualize them on the inflated >>>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>>> same hemisphere/subject and visualize it on any other >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>>> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>>> this new ROI surface? >>>>>>> >>>>>>> Thanks, >>>>>>> Anna >>>>>>> >>>>>>> =================================== >>>>>>> >>>>>>> Please consider the environment before printing this e-mail >>>>>>> >>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>>> electronic or hard copy. Thank you. >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> 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. >>>>>> >>>>>> >>>>>> =================================== >>>>>> >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>> >>>>>> >>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote:
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label.
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=<path>
On 9/27/16 11:31 AM, Crawford, Anna wrote: > I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. > > bash: setenv: command not found > > Thanks, > Anna > ________________________________________ > From: Crawford, Anna > Sent: Tuesday, September 27, 2016 11:12 AM > To: Freesurfer support list > Subject: RE: [Freesurfer] Co-registering different source data > > If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. > > Thanks, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] > Sent: Tuesday, September 27, 2016 10:50 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Co-registering different source data > > Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that > is already set properly, then do not use the --sd. > > > On 9/27/16 9:38 AM, Crawford, Anna wrote: >> Hi, >> >> I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? >> >> Thank you, >> Anna >> >> >> mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume >> >> srclabel = Testing.label >> srcsubject = segfs >> trgsubject = segfs >> trglabel = Testing1N.label >> regmethod = volume >> >> usehash = 1 >> Use ProjAbs = 0, 0 >> Use ProjFrac = 0, 0 >> DoPaint 0 >> >> SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >> FREESURFER_HOME /tools/freesurfer >> Loading source label. >> No such file or directory >> mri_label2label: could not open label file Testing.label >> No such file or directory >> ERROR reading Testing.label >> >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 6:20 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Hi Anna >> >> freeview now checks (in the dev version I believe) if the label has been >> sampled onto the surface and won't crash, but you need to use >> mri_label2label to sample it onto the surface before loading it onto the >> inflated surface in freeview >> >> cheers >> Bruce >> >> >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> Hi, >>> >>> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >>> >>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >>> >>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>> >>> among other similar variations. Am I just inputting it wrong or am I just missing information? >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 4:23 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> scuba is very old and deprecated. Try using freeview instead >>> >>> cheers >>> Bruce >>> On Mon, 26 Sep >>> 2016, Crawford, Anna wrote: >>> >>>> To create the volume ROI, I found something that said to use: >>>> >>>> scuba -v $filename >>>> >>>> to then make a new ROI. >>>> >>>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 1:52 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> yes, create a volume ROI and you can map it onto the surface using >>>> mri_vol2surf >>>> >>>> cheers >>>> Bruce >>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>> >>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>>> >>>>> Thank you, >>>>> Anna >>>>> ________________________________________ >>>>> >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 1:16 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> can you explain what the ROI is supposed to represent? If you can create >>>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>>> >>>>>> Thanks, >>>>>> Anna >>>>>> ________________________________________ >>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>> >>>>>> Hi Anna >>>>>> >>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>>> the white or pial surface, then you can visualize them on the inflated >>>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>>> same hemisphere/subject and visualize it on any other >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>>> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>>> this new ROI surface? >>>>>>> >>>>>>> Thanks, >>>>>>> Anna >>>>>>> >>>>>>> =================================== >>>>>>> >>>>>>> Please consider the environment before printing this e-mail >>>>>>> >>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>>> electronic or hard copy. Thank you. >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> 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. >>>>>> >>>>>> >>>>>> =================================== >>>>>> >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>> >>>>>> >>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
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can you email me (offlist) the inflated surface and the label you tried to load? On Wed, 28 Sep 2016, Crawford, Anna wrote:
The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote:
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote: > Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label. > > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] > Sent: Tuesday, September 27, 2016 11:36 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Anna, if you are using bash the command is: > > export SUBJECTS_DIR=<path> > > > On 9/27/16 11:31 AM, Crawford, Anna wrote: >> I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. >> >> bash: setenv: command not found >> >> Thanks, >> Anna >> ________________________________________ >> From: Crawford, Anna >> Sent: Tuesday, September 27, 2016 11:12 AM >> To: Freesurfer support list >> Subject: RE: [Freesurfer] Co-registering different source data >> >> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. >> >> Thanks, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 27, 2016 10:50 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that >> is already set properly, then do not use the --sd. >> >> >> On 9/27/16 9:38 AM, Crawford, Anna wrote: >>> Hi, >>> >>> I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? >>> >>> Thank you, >>> Anna >>> >>> >>> mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume >>> >>> srclabel = Testing.label >>> srcsubject = segfs >>> trgsubject = segfs >>> trglabel = Testing1N.label >>> regmethod = volume >>> >>> usehash = 1 >>> Use ProjAbs = 0, 0 >>> Use ProjFrac = 0, 0 >>> DoPaint 0 >>> >>> SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >>> FREESURFER_HOME /tools/freesurfer >>> Loading source label. >>> No such file or directory >>> mri_label2label: could not open label file Testing.label >>> No such file or directory >>> ERROR reading Testing.label >>> >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 6:20 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> freeview now checks (in the dev version I believe) if the label has been >>> sampled onto the surface and won't crash, but you need to use >>> mri_label2label to sample it onto the surface before loading it onto the >>> inflated surface in freeview >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >>>> >>>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >>>> >>>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>>> >>>> among other similar variations. Am I just inputting it wrong or am I just missing information? >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 4:23 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> scuba is very old and deprecated. Try using freeview instead >>>> >>>> cheers >>>> Bruce >>>> On Mon, 26 Sep >>>> 2016, Crawford, Anna wrote: >>>> >>>>> To create the volume ROI, I found something that said to use: >>>>> >>>>> scuba -v $filename >>>>> >>>>> to then make a new ROI. >>>>> >>>>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>>>> >>>>> Thank you, >>>>> Anna >>>>> ________________________________________ >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 1:52 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> yes, create a volume ROI and you can map it onto the surface using >>>>> mri_vol2surf >>>>> >>>>> cheers >>>>> Bruce >>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>> >>>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>>>> >>>>>> Thank you, >>>>>> Anna >>>>>> ________________________________________ >>>>>> >>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>> Sent: Monday, September 26, 2016 1:16 PM >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>> >>>>>> can you explain what the ROI is supposed to represent? If you can create >>>>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>>>> >>>>>>> Thanks, >>>>>>> Anna >>>>>>> ________________________________________ >>>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>>>> To: Freesurfer support list >>>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>>> >>>>>>> Hi Anna >>>>>>> >>>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>>>> the white or pial surface, then you can visualize them on the inflated >>>>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>>>> same hemisphere/subject and visualize it on any other >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>>>> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>>>> this new ROI surface? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Anna >>>>>>>> >>>>>>>> =================================== >>>>>>>> >>>>>>>> Please consider the environment before printing this e-mail >>>>>>>> >>>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>>>> electronic or hard copy. Thank you. >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> 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. >>>>>>> >>>>>>> >>>>>>> =================================== >>>>>>> >>>>>>> >>>>>>> Please consider the environment before printing this e-mail >>>>>>> >>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>>> >>>>>>> >>>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> =================================== >>>>>> >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>> >>>>>> >>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. 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If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. 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Is Testing1.label a surface-based label? If so, use --regmethod surface
On 09/28/2016 04:39 PM, Crawford, Anna wrote:
The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote:
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote: > Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label. > > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] > Sent: Tuesday, September 27, 2016 11:36 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Anna, if you are using bash the command is: > > export SUBJECTS_DIR=<path> > > > On 9/27/16 11:31 AM, Crawford, Anna wrote: >> I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. >> >> bash: setenv: command not found >> >> Thanks, >> Anna >> ________________________________________ >> From: Crawford, Anna >> Sent: Tuesday, September 27, 2016 11:12 AM >> To: Freesurfer support list >> Subject: RE: [Freesurfer] Co-registering different source data >> >> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. >> >> Thanks, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 27, 2016 10:50 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that >> is already set properly, then do not use the --sd. >> >> >> On 9/27/16 9:38 AM, Crawford, Anna wrote: >>> Hi, >>> >>> I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? >>> >>> Thank you, >>> Anna >>> >>> >>> mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume >>> >>> srclabel = Testing.label >>> srcsubject = segfs >>> trgsubject = segfs >>> trglabel = Testing1N.label >>> regmethod = volume >>> >>> usehash = 1 >>> Use ProjAbs = 0, 0 >>> Use ProjFrac = 0, 0 >>> DoPaint 0 >>> >>> SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >>> FREESURFER_HOME /tools/freesurfer >>> Loading source label. >>> No such file or directory >>> mri_label2label: could not open label file Testing.label >>> No such file or directory >>> ERROR reading Testing.label >>> >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 6:20 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> freeview now checks (in the dev version I believe) if the label has been >>> sampled onto the surface and won't crash, but you need to use >>> mri_label2label to sample it onto the surface before loading it onto the >>> inflated surface in freeview >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >>>> >>>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >>>> >>>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>>> >>>> among other similar variations. Am I just inputting it wrong or am I just missing information? >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 4:23 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> scuba is very old and deprecated. Try using freeview instead >>>> >>>> cheers >>>> Bruce >>>> On Mon, 26 Sep >>>> 2016, Crawford, Anna wrote: >>>> >>>>> To create the volume ROI, I found something that said to use: >>>>> >>>>> scuba -v $filename >>>>> >>>>> to then make a new ROI. >>>>> >>>>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>>>> >>>>> Thank you, >>>>> Anna >>>>> ________________________________________ >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 1:52 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> yes, create a volume ROI and you can map it onto the surface using >>>>> mri_vol2surf >>>>> >>>>> cheers >>>>> Bruce >>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>> >>>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>>>> >>>>>> Thank you, >>>>>> Anna >>>>>> ________________________________________ >>>>>> >>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>> Sent: Monday, September 26, 2016 1:16 PM >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>> >>>>>> can you explain what the ROI is supposed to represent? If you can create >>>>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>>>> >>>>>>> Thanks, >>>>>>> Anna >>>>>>> ________________________________________ >>>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>>>> To: Freesurfer support list >>>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>>> >>>>>>> Hi Anna >>>>>>> >>>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>>>> the white or pial surface, then you can visualize them on the inflated >>>>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>>>> same hemisphere/subject and visualize it on any other >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>>>> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>>>> this new ROI surface? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Anna >>>>>>>> >>>>>>>> =================================== >>>>>>>> >>>>>>>> Please consider the environment before printing this e-mail >>>>>>>> >>>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>>>> electronic or hard copy. Thank you. >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> 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. >>>>>>> >>>>>>> >>>>>>> =================================== >>>>>>> >>>>>>> >>>>>>> Please consider the environment before printing this e-mail >>>>>>> >>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>>> >>>>>>> >>>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> =================================== >>>>>> >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>> >>>>>> >>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
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Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I get a different error when I use --regmethod surface (below). I double checked that I am in the correct hemishpere. I'm not sure if it has to do with teh volume I used to draw to ROI or something with how I drew it.
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1Ns.label --regmethod surface --hemi lh
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1Ns.label regmethod = surface
srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting surface-based mapping Reading source registration /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Reading target registration /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 0: vno = -1, max = 115984
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 5:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Is Testing1.label a surface-based label? If so, use --regmethod surface
On 09/28/2016 04:39 PM, Crawford, Anna wrote:
The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote:
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
Th output is below:
aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
Thanks, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote: > Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label. > > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] > Sent: Tuesday, September 27, 2016 11:36 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Anna, if you are using bash the command is: > > export SUBJECTS_DIR=<path> > > > On 9/27/16 11:31 AM, Crawford, Anna wrote: >> I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. >> >> bash: setenv: command not found >> >> Thanks, >> Anna >> ________________________________________ >> From: Crawford, Anna >> Sent: Tuesday, September 27, 2016 11:12 AM >> To: Freesurfer support list >> Subject: RE: [Freesurfer] Co-registering different source data >> >> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. >> >> Thanks, >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 27, 2016 10:50 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that >> is already set properly, then do not use the --sd. >> >> >> On 9/27/16 9:38 AM, Crawford, Anna wrote: >>> Hi, >>> >>> I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? >>> >>> Thank you, >>> Anna >>> >>> >>> mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume >>> >>> srclabel = Testing.label >>> srcsubject = segfs >>> trgsubject = segfs >>> trglabel = Testing1N.label >>> regmethod = volume >>> >>> usehash = 1 >>> Use ProjAbs = 0, 0 >>> Use ProjFrac = 0, 0 >>> DoPaint 0 >>> >>> SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >>> FREESURFER_HOME /tools/freesurfer >>> Loading source label. >>> No such file or directory >>> mri_label2label: could not open label file Testing.label >>> No such file or directory >>> ERROR reading Testing.label >>> >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 6:20 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Hi Anna >>> >>> freeview now checks (in the dev version I believe) if the label has been >>> sampled onto the surface and won't crash, but you need to use >>> mri_label2label to sample it onto the surface before loading it onto the >>> inflated surface in freeview >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >>>> >>>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >>>> >>>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>>> >>>> among other similar variations. Am I just inputting it wrong or am I just missing information? >>>> >>>> Thank you, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 4:23 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> scuba is very old and deprecated. Try using freeview instead >>>> >>>> cheers >>>> Bruce >>>> On Mon, 26 Sep >>>> 2016, Crawford, Anna wrote: >>>> >>>>> To create the volume ROI, I found something that said to use: >>>>> >>>>> scuba -v $filename >>>>> >>>>> to then make a new ROI. >>>>> >>>>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>>>> >>>>> Thank you, >>>>> Anna >>>>> ________________________________________ >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 1:52 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> yes, create a volume ROI and you can map it onto the surface using >>>>> mri_vol2surf >>>>> >>>>> cheers >>>>> Bruce >>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>> >>>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>>>> >>>>>> Thank you, >>>>>> Anna >>>>>> ________________________________________ >>>>>> >>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>> Sent: Monday, September 26, 2016 1:16 PM >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>> >>>>>> can you explain what the ROI is supposed to represent? If you can create >>>>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>>>> >>>>>>> Thanks, >>>>>>> Anna >>>>>>> ________________________________________ >>>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>>>> To: Freesurfer support list >>>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>>> >>>>>>> Hi Anna >>>>>>> >>>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>>>> the white or pial surface, then you can visualize them on the inflated >>>>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>>>> same hemisphere/subject and visualize it on any other >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>>>> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>>>> this new ROI surface? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Anna >>>>>>>> >>>>>>>> =================================== >>>>>>>> >>>>>>>> Please consider the environment before printing this e-mail >>>>>>>> >>>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>>>> Report (2015). 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If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> =================================== >>>>>> >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>> >>>>>> >>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. 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If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Can you send me the label?
On 09/28/2016 05:54 PM, Crawford, Anna wrote:
I get a different error when I use --regmethod surface (below). I double checked that I am in the correct hemishpere. I'm not sure if it has to do with teh volume I used to draw to ROI or something with how I drew it.
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1Ns.label --regmethod surface --hemi lh
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1Ns.label regmethod = surface
srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting surface-based mapping Reading source registration /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Reading target registration /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created. Label point 0: vno = -1, max = 115984
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 5:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Is Testing1.label a surface-based label? If so, use --regmethod surface
On 09/28/2016 04:39 PM, Crawford, Anna wrote:
The subject path was /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which subject? On Wed, 28 Sep 2016, Crawford, Anna wrote:
I just opened freeview (just typed freeview into the command line). Then from inside freeview, under the surfaces tab, I loaded the lh.inflated and rh.inflated. Also under the surfaces tab, under Label I chose the label file created (Testing1N.label). When I tried to open the label, is when Freeview crashed.
Thanks,
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
Thank you! that seemed to have worked. I thought I had tried that before, but must not that. The input/output is below. The new label was created. When I tried to load the label onto the surface, FreeView crashed the same as it did before though which brings me back to my original problem on Freeview crashing when I try to put the label on the surface. Do I need to change the label to a volume/surface to get this to work?
Thanks,
Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label [crawforda@fmri2 ~]$ mri_label2label --srcsubject segfs --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. Found 216 points in source label. Starting volumetric mapping 216 points Src2TrgVolReg: ----------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 -0.000; 0.000 -0.000 1.000 -0.000; 0.000 0.000 0.000 1.000; 0 -39.0000 17.0000 55.0000 -39.0000 17.0000 55.0000 1 -38.0000 17.0000 55.0000 -38.0000 17.0000 55.0000 2 -40.0000 18.0000 55.0000 -40.0000 18.0000 55.0000 3 -39.0000 18.0000 55.0000 -39.0000 18.0000 55.0000 4 -38.0000 18.0000 55.0000 -38.0000 18.0000 55.0000 Writing label file Testing1N.label 216 mri_label2label: Done
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
Hi,
Below is the command I entered with the output containing the error. I also tried different variations on the path for the directory, but this is the one I thought it should be.
Thanks, Anna
mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume
srclabel = Testing1.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume
usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing1.label No such file or directory ERROR reading Testing1.label ______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2016 3:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full screen output of the command you tried to run and the error it gives?
thanks Bruce On Tue, 27 Sep 2016, Crawford, Anna wrote:
I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the subject was segfs, and then the file I wanted to use. I thought it would be the same in the case in that regard, but it doesn't seem to be working that way.
Thank you, Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] Sent: Tuesday, September 27, 2016 12:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label
hth d
On 9/27/16 11:58 AM, Crawford, Anna wrote: > Th output is below: > > aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label > aparc.annot.ctab lh.BA45.thresh.label rh.aparc.a2009s.annot rh.BA4p.thresh.label > aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot rh.BA6.label > BA.ctab lh.BA4a.thresh.label rh.aparc.DKTatlas40.annot rh.BA6.thresh.label > BA.thresh.ctab lh.BA4p.label rh.BA1.label rh.BA.annot > lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label rh.BA.thresh.annot > lh.aparc.annot lh.BA6.label rh.BA2.label rh.cortex.label > lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label rh.entorhinal_exvivo.label > lh.BA1.label lh.BA.annot rh.BA3a.label rh.MT.label > lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label rh.MT.thresh.label > lh.BA2.label lh.cortex.label rh.BA3b.label rh.perirhinal.label > lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label rh.V1.label > lh.BA3a.label lh.MT.label rh.BA44.label rh.V1.thresh.label > lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label rh.V2.label > lh.BA3b.label lh.perirhinal.label rh.BA45.label rh.V2.thresh.label > lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label Testing1.label > lh.BA44.label lh.V1.thresh.label rh.BA4a.label Testing.label > lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label > > Thanks, > Anna > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] > Sent: Tuesday, September 27, 2016 11:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > what is the output of "ls"? > > > On 9/27/16 11:50 AM, Crawford, Anna wrote: >> Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label. >> >> Anna >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman@gmail.com] >> Sent: Tuesday, September 27, 2016 11:36 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Anna, if you are using bash the command is: >> >> export SUBJECTS_DIR=<path> >> >> >> On 9/27/16 11:31 AM, Crawford, Anna wrote: >>> I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. >>> >>> bash: setenv: command not found >>> >>> Thanks, >>> Anna >>> ________________________________________ >>> From: Crawford, Anna >>> Sent: Tuesday, September 27, 2016 11:12 AM >>> To: Freesurfer support list >>> Subject: RE: [Freesurfer] Co-registering different source data >>> >>> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. >>> >>> Thanks, >>> Anna >>> ________________________________________ >>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] >>> Sent: Tuesday, September 27, 2016 10:50 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that >>> is already set properly, then do not use the --sd. >>> >>> >>> On 9/27/16 9:38 AM, Crawford, Anna wrote: >>>> Hi, >>>> >>>> I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it? >>>> >>>> Thank you, >>>> Anna >>>> >>>> >>>> mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume >>>> >>>> srclabel = Testing.label >>>> srcsubject = segfs >>>> trgsubject = segfs >>>> trglabel = Testing1N.label >>>> regmethod = volume >>>> >>>> usehash = 1 >>>> Use ProjAbs = 0, 0 >>>> Use ProjFrac = 0, 0 >>>> DoPaint 0 >>>> >>>> SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label >>>> FREESURFER_HOME /tools/freesurfer >>>> Loading source label. >>>> No such file or directory >>>> mri_label2label: could not open label file Testing.label >>>> No such file or directory >>>> ERROR reading Testing.label >>>> >>>> ________________________________________ >>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 6:20 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> freeview now checks (in the dev version I believe) if the label has been >>>> sampled onto the surface and won't crash, but you need to use >>>> mri_label2label to sample it onto the surface before loading it onto the >>>> inflated surface in freeview >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>> >>>>> Hi, >>>>> >>>>> i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? >>>>> >>>>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an errorL option unknown. I did the following: >>>>> >>>>> mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz >>>>> >>>>> among other similar variations. Am I just inputting it wrong or am I just missing information? >>>>> >>>>> Thank you, >>>>> Anna >>>>> ________________________________________ >>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>> Sent: Monday, September 26, 2016 4:23 PM >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>> >>>>> Hi Anna >>>>> >>>>> scuba is very old and deprecated. Try using freeview instead >>>>> >>>>> cheers >>>>> Bruce >>>>> On Mon, 26 Sep >>>>> 2016, Crawford, Anna wrote: >>>>> >>>>>> To create the volume ROI, I found something that said to use: >>>>>> >>>>>> scuba -v $filename >>>>>> >>>>>> to then make a new ROI. >>>>>> >>>>>> I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? >>>>>> >>>>>> Thank you, >>>>>> Anna >>>>>> ________________________________________ >>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>> Sent: Monday, September 26, 2016 1:52 PM >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>> >>>>>> yes, create a volume ROI and you can map it onto the surface using >>>>>> mri_vol2surf >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>>> >>>>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active region that I want to capture and then map it to the surface. First, I want to be sure that I can get an ROI that I can then project to the surface (which I assume would be something like mri_vol2surf) if that makes sense. So i first need to be able to create the volume or label. >>>>>>> >>>>>>> Thank you, >>>>>>> Anna >>>>>>> ________________________________________ >>>>>>> >>>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>>> Sent: Monday, September 26, 2016 1:16 PM >>>>>>> To: Freesurfer support list >>>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>>> >>>>>>> can you explain what the ROI is supposed to represent? If you can create >>>>>>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Anna >>>>>>>> ________________________________________ >>>>>>>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>>>>>> Sent: Monday, September 26, 2016 10:44 AM >>>>>>>> To: Freesurfer support list >>>>>>>> Subject: Re: [Freesurfer] Co-registering different source data >>>>>>>> >>>>>>>> Hi Anna >>>>>>>> >>>>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>>>>>> the white or pial surface, then you can visualize them on the inflated >>>>>>>> surface trivially. That is, you can create your ROI on any surface of the >>>>>>>> same hemisphere/subject and visualize it on any other >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> >>>>>>>> On Mon, 26 Sep 2016, Crawford, Anna >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hello, >>>>>>>>> >>>>>>>>> I am trying to create a new surface area on the inflated brain given by freesurfer >>>>>>>>> using recon-all. I make to create my own ROI that is co-registered onto this surfer. >>>>>>>>> Ultimately, I want to be able to take information from a different data source such as >>>>>>>>> EEG and have it co-registered onto the inflated surface. How do I go about creating >>>>>>>>> this new ROI surface? >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Anna >>>>>>>>> >>>>>>>>> =================================== >>>>>>>>> >>>>>>>>> Please consider the environment before printing this e-mail >>>>>>>>> >>>>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World >>>>>>>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing >>>>>>>>> of our services, staff and locations. Confidentiality Note: This message is intended >>>>>>>>> for use only by the individual or entity to which it is addressed and may contain >>>>>>>>> information that is privileged, confidential, and exempt from disclosure under >>>>>>>>> applicable law. If the reader of this message is not the intended recipient or the >>>>>>>>> employee or agent responsible for delivering the message to the intended recipient, you >>>>>>>>> are hereby notified that any dissemination, distribution or copying of this >>>>>>>>> communication is strictly prohibited. If you have received this communication in error, >>>>>>>>> please contact the sender immediately and destroy the material in its entirety, whether >>>>>>>>> electronic or hard copy. 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If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>>>> >>>>>>>> Thank you. >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> =================================== >>>>>>> >>>>>>> >>>>>>> Please consider the environment before printing this e-mail >>>>>>> >>>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>>> >>>>>>> >>>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> =================================== >>>>>> >>>>>> >>>>>> Please consider the environment before printing this e-mail >>>>>> >>>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>>> >>>>>> >>>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> =================================== >>>>> >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>>> >>>>> >>>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>>> >>>>> Thank you. >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> =================================== >>>> >>>> >>>> Please consider the environment before printing this e-mail >>>> >>>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>>> >>>> >>>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>>> >>>> Thank you. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> =================================== >>> >>> >>> Please consider the environment before printing this e-mail >>> >>> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >>> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >>> >>> >>> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. > > Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mailCleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
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 greve@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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Crawford, Anna -
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Douglas Greve -
Douglas N Greve