Dear Freesurfer experts,
While the recon-all stream makes it easy to map gyri onto specific voxels via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth.
The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere.
My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer.
Cheers, Jordan
____________________ Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk@princeton.edu
Hi Jordan
we don't really compute the middle of the gyrus or crown or anything. tksurfer does have a plot_curv function that allows you to click on a set of points on the surface (inflated is probably easiest), then type
plot_curv 0
at the tcl (%) prompt, and tksurfer will then compute the shortest edge-based path connecting the ordered set of points and write a datafile named "surfer_curv.dat" with entries:
vno x y z distance curv val val2 stat amp deg normalized_deg radians
so if you have an overlay loaded it will show up in the 7th column (I think).
cheers Bruce
On Sat, 4 Feb 2012, Jordan Poppenk wrote:
Dear Freesurfer experts,
While the recon-all stream makes it easy to map gyri onto specific voxels
via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth.
The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere.
My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer.
Cheers, Jordan
Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk@princeton.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
Thanks for your response and for the suggestion. Your solution sounds great for a small number of regions or individuals. The trouble is that I am looking for a way to track most of the gyri across many individuals, and introducing a manual intervention at any stage would make this very time consuming.
If not the gyrus crown, does FS perhaps trace sulci at some stage to help it classify gyri? Or, if there is no way to obtain this info directly from FS, maybe I could combine the depth info produced in the inflation stage with the label data to estimate gyrus boundaries on my own. Do you think there is likely to be enough information to make this work reliably? Do you have any cautionary advice about using the depth info to identify sulci in an automated fashion?
Cheers, Jordan
On Feb 4, 2012, at 6:42 PM, Bruce Fischl wrote:
Hi Jordan
we don't really compute the middle of the gyrus or crown or anything. tksurfer does have a plot_curv function that allows you to click on a set of points on the surface (inflated is probably easiest), then type
plot_curv 0
at the tcl (%) prompt, and tksurfer will then compute the shortest edge-based path connecting the ordered set of points and write a datafile named "surfer_curv.dat" with entries:
vno x y z distance curv val val2 stat amp deg normalized_deg radians
so if you have an overlay loaded it will show up in the 7th column (I think).
cheers Bruce
On Sat, 4 Feb 2012, Jordan Poppenk wrote:
Dear Freesurfer experts,
While the recon-all stream makes it easy to map gyri onto specific voxels
via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth.
The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere.
My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer.
Cheers, Jordan
Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk@princeton.edu
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 Jordan
people have tried using the Hessian to define crowns, but it's hard to estimate stably. If I were you I think I would draw a label on fsaverage in the order you want, then map that to each subject in your dataset and use it to extra the measures you want. I think it should preserve the ordering Bruce
On Mon, 6 Feb 2012, Jordan Poppenk wrote:
Dear Bruce,
Thanks for your response and for the suggestion. Your solution sounds great for a small number of regions or individuals. The trouble is that I am looking for a way to track most of the gyri across many individuals, and introducing a manual intervention at any stage would make this very time consuming.
If not the gyrus crown, does FS perhaps trace sulci at some stage to help it classify gyri? Or, if there is no way to obtain this info directly from FS, maybe I could combine the depth info produced in the inflation stage with the label data to estimate gyrus boundaries on my own. Do you think there is likely to be enough information to make this work reliably? Do you have any cautionary advice about using the depth info to identify sulci in an automated fashion?
Cheers, Jordan
On Feb 4, 2012, at 6:42 PM, Bruce Fischl wrote:
Hi Jordan
we don't really compute the middle of the gyrus or crown or anything. tksurfer does have a plot_curv function that allows you to click on a set of points on the surface (inflated is probably easiest), then type
plot_curv 0
at the tcl (%) prompt, and tksurfer will then compute the shortest edge-based path connecting the ordered set of points and write a datafile named "surfer_curv.dat" with entries:
vno x y z distance curv val val2 stat amp deg normalized_deg radians
so if you have an overlay loaded it will show up in the 7th column (I think).
cheers Bruce
On Sat, 4 Feb 2012, Jordan Poppenk wrote:
Dear Freesurfer experts,
While the recon-all stream makes it easy to map gyri onto specific voxels
via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth.
The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere.
My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer.
Cheers, Jordan
Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk@princeton.edu
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 Bruce,
Do you know if the Hessian on height data for sulci is any more stable? That approach would also work well for my purposes.
If not, just to make sure I understand your suggestion, to help follow gyri on one of the existing atlases (e.g., aparc), I will: 1) trace the crowns on the fsaverage version of that atlas by editing the fsaverage label file and stripping all non-crown voxels (relabeling as "unknown"), then save as a new label file 2) use the subject-wise transform computed by FS for the original atlas to propagate the revised label file to each subject
Cheers, Jordan
On Feb 6, 2012, at 9:32 AM, Bruce Fischl wrote:
Hi Jordan
people have tried using the Hessian to define crowns, but it's hard to estimate stably. If I were you I think I would draw a label on fsaverage in the order you want, then map that to each subject in your dataset and use it to extra the measures you want. I think it should preserve the ordering Bruce
On Mon, 6 Feb 2012, Jordan Poppenk wrote:
Dear Bruce,
Thanks for your response and for the suggestion. Your solution sounds great for a small number of regions or individuals. The trouble is that I am looking for a way to track most of the gyri across many individuals, and introducing a manual intervention at any stage would make this very time consuming.
If not the gyrus crown, does FS perhaps trace sulci at some stage to help it classify gyri? Or, if there is no way to obtain this info directly from FS, maybe I could combine the depth info produced in the inflation stage with the label data to estimate gyrus boundaries on my own. Do you think there is likely to be enough information to make this work reliably? Do you have any cautionary advice about using the depth info to identify sulci in an automated fashion?
Cheers, Jordan
On Feb 4, 2012, at 6:42 PM, Bruce Fischl wrote:
Hi Jordan
we don't really compute the middle of the gyrus or crown or anything. tksurfer does have a plot_curv function that allows you to click on a set of points on the surface (inflated is probably easiest), then type
plot_curv 0
at the tcl (%) prompt, and tksurfer will then compute the shortest edge-based path connecting the ordered set of points and write a datafile named "surfer_curv.dat" with entries:
vno x y z distance curv val val2 stat amp deg normalized_deg radians
so if you have an overlay loaded it will show up in the 7th column (I think).
cheers Bruce
On Sat, 4 Feb 2012, Jordan Poppenk wrote:
Dear Freesurfer experts,
While the recon-all stream makes it easy to map gyri onto specific voxels
via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth.
The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere.
My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer.
Cheers, Jordan
Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk@princeton.edu
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 Jordan
do you mean for a specific gyrus or for lots of them? Bruce
On Mon, 6 Feb 2012, Jordan Poppenk wrote:
Hi Bruce,
Do you know if the Hessian on height data for sulci is any more stable? That approach would also work well for my purposes.
If not, just to make sure I understand your suggestion, to help follow gyri on one of the existing atlases (e.g., aparc), I will:
- trace the crowns on the fsaverage version of that atlas by editing the fsaverage label file and stripping all non-crown voxels (relabeling as "unknown"), then save as a new label file
- use the subject-wise transform computed by FS for the original atlas to propagate the revised label file to each subject
Cheers, Jordan
On Feb 6, 2012, at 9:32 AM, Bruce Fischl wrote:
Hi Jordan
people have tried using the Hessian to define crowns, but it's hard to estimate stably. If I were you I think I would draw a label on fsaverage in the order you want, then map that to each subject in your dataset and use it to extra the measures you want. I think it should preserve the ordering Bruce
On Mon, 6 Feb 2012, Jordan Poppenk wrote:
Dear Bruce,
Thanks for your response and for the suggestion. Your solution sounds great for a small number of regions or individuals. The trouble is that I am looking for a way to track most of the gyri across many individuals, and introducing a manual intervention at any stage would make this very time consuming.
If not the gyrus crown, does FS perhaps trace sulci at some stage to help it classify gyri? Or, if there is no way to obtain this info directly from FS, maybe I could combine the depth info produced in the inflation stage with the label data to estimate gyrus boundaries on my own. Do you think there is likely to be enough information to make this work reliably? Do you have any cautionary advice about using the depth info to identify sulci in an automated fashion?
Cheers, Jordan
On Feb 4, 2012, at 6:42 PM, Bruce Fischl wrote:
Hi Jordan
we don't really compute the middle of the gyrus or crown or anything. tksurfer does have a plot_curv function that allows you to click on a set of points on the surface (inflated is probably easiest), then type
plot_curv 0
at the tcl (%) prompt, and tksurfer will then compute the shortest edge-based path connecting the ordered set of points and write a datafile named "surfer_curv.dat" with entries:
vno x y z distance curv val val2 stat amp deg normalized_deg radians
so if you have an overlay loaded it will show up in the 7th column (I think).
cheers Bruce
On Sat, 4 Feb 2012, Jordan Poppenk wrote:
Dear Freesurfer experts,
While the recon-all stream makes it easy to map gyri onto specific voxels
via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth.
The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere.
My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer.
Cheers, Jordan
Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk@princeton.edu
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Jordan Poppenk