Hi,
I am almost there and now need to produce what you might call an atlas for an individual. I have a large set of current source locations extracted from MEG recordings for each volunteer. They are in the individual's RAS MRI coordinates so I can easily convert them to tkr or another of the coordinate systems used by freesurfer. I then need to find or create a tool to which I can hand that vector and get back the labels which have been assigned to it. Can you see a way to do it with existing freesurfer tools, even if it's awkward?
Thanks,
Don
Hi Don
what kind of label do you mean? Volume (aseg) or surface (annot). I guess you could just pick out the aparc+aseg.mgz label and get both.
cheers Bruce
On Fri, 8 Aug 2014, Krieger, Donald N. wrote:
Hi,
I am almost there and now need to produce what you might call an atlas for an individual. I have a large set of current source locations extracted from MEG recordings for each volunteer. They are in the individual's RAS MRI coordinates so I can easily convert them to tkr or another of the coordinate systems used by freesurfer. I then need to find or create a tool to which I can hand that vector and get back the labels which have been assigned to it. Can you see a way to do it with existing freesurfer tools, even if it's awkward?
Thanks,
Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks for responding so quickly. I think it's the volume label I want although honestly, I'm still not confident that I understand the language. The vectors for which I need the associated label(s) can be almost anywhere in the volume of the head. And for each one, I need to get the label(s) for the nearest vector that freesurfer has identified. It would work for my purpose if that label was for the nearest vector on a surface, particularly orig, white, or pial.
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, August 08, 2014 11:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?
Hi Don
what kind of label do you mean? Volume (aseg) or surface (annot). I guess you could just pick out the aparc+aseg.mgz label and get both.
cheers Bruce
On Fri, 8 Aug 2014, Krieger, Donald N. wrote:
Hi,
I am almost there and now need to produce what you might call an atlas for an individual. I have a large set of current source locations extracted from MEG recordings for each volunteer. They are in the individual's RAS MRI coordinates so I can easily convert them to tkr or another of the coordinate systems used by freesurfer. I then need to find or create a tool to which I can hand that vector and get back the labels which have been assigned to it. Can you see a way to do it with existing freesurfer tools, even if it's awkward?
Thanks,
Don
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Don
you have to decide what you want! What does the "nearest surface label" mean? If you are outside of brain do you want to project onto the cortex and find that label? What if you are in the middle of caudate for example?
cheers Bruce
On Fri, 8 Aug 2014, Krieger, Donald N. wrote:
Hi Bruce,
Thanks for responding so quickly. I think it's the volume label I want although honestly, I'm still not confident that I understand the language. The vectors for which I need the associated label(s) can be almost anywhere in the volume of the head. And for each one, I need to get the label(s) for the nearest vector that freesurfer has identified. It would work for my purpose if that label was for the nearest vector on a surface, particularly orig, white, or pial.
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, August 08, 2014 11:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?
Hi Don
what kind of label do you mean? Volume (aseg) or surface (annot). I guess you could just pick out the aparc+aseg.mgz label and get both.
cheers Bruce
On Fri, 8 Aug 2014, Krieger, Donald N. wrote:
Hi,
I am almost there and now need to produce what you might call an atlas for an individual. I have a large set of current source locations extracted from MEG recordings for each volunteer. They are in the individual's RAS MRI coordinates so I can easily convert them to tkr or another of the coordinate systems used by freesurfer. I then need to find or create a tool to which I can hand that vector and get back the labels which have been assigned to it. Can you see a way to do it with existing freesurfer tools, even if it's awkward?
Thanks,
Don
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think I'm up against my ignorance here. But it seems fairly clear that what I need is to pass the vector to the tool in a form where the tool will come back with label(s) for that precise location or return something like "unknown." So if it's outside the head ... "unknown" If it's in the caudate ... "caudate" If it's in Right V1 gray ... rh.V1.orig. If it's in Right V1 white ... rh.V1.white.
Does that make sense? Honestly I'm not quite sure because I haven't fooled around with the different labelled vectors enough to figure out when to expect something on a surface vs something in the volume. I'm happy to try for both if that's needed depending on the region since there do not appear to be volume labels for many regions in aseg.mgz . I apologize for being slow on the uptake here but there are several things about freesurfer that I still don't get.
Don
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, August 08, 2014 11:38 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?
Hi Don
you have to decide what you want! What does the "nearest surface label" mean? If you are outside of brain do you want to project onto the cortex and find that label? What if you are in the middle of caudate for example?
cheers Bruce
On Fri, 8 Aug 2014, Krieger, Donald N. wrote:
Hi Bruce,
Thanks for responding so quickly. I think it's the volume label I want although honestly, I'm still not confident that I understand the language. The vectors for which I need the associated label(s) can be almost anywhere in the volume of the head. And for each one, I need to get the label(s) for the nearest vector that freesurfer has identified. It would work for my purpose if that label was for the nearest vector on a surface, particularly orig, white, or pial.
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, August 08, 2014 11:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tool which will return the labels associated with a RAS vector ?
Hi Don
what kind of label do you mean? Volume (aseg) or surface (annot). I guess you could just pick out the aparc+aseg.mgz label and get both.
cheers Bruce
On Fri, 8 Aug 2014, Krieger, Donald N. wrote:
Hi,
I am almost there and now need to produce what you might call an atlas for an individual. I have a large set of current source locations extracted from MEG recordings for each volunteer. They are in the individual's RAS MRI coordinates so I can easily convert them to tkr or another of the coordinate systems used by freesurfer. I then need to find or create a tool to which I can hand that vector and get back the labels which have been assigned to it. Can you see a way to do it with existing freesurfer tools, even if it's awkward?
Thanks,
Don
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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 -
Krieger, Donald N.