I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Bruce. I just checked the TkSurferGuide and noticed that it says the scale bar is 1mm (which looks about right). However, while the scale bar at the default zoom looks fine, I find that it's length behaves strangely (it shrinks) when I zoom into the image. Does the distance value change, or might there be something wrong with my display?
Eric
On Mar 25, 2010, at 11:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Hi Eric,
it doesn't shrink for me, it expands. And I'm pretty sure it's 1cm, not 1mm (which is about the vertex spacing), so the guide must be wrong. We'll fix it
Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
Thanks Bruce. I just checked the TkSurferGuide and noticed that it says the scale bar is 1mm (which looks about right). However, while the scale bar at the default zoom looks fine, I find that it's length behaves strangely (it shrinks) when I zoom into the image. Does the distance value change, or might there be something wrong with my display?
Eric
On Mar 25, 2010, at 11:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
That's peculiar. I suppose it's somehow related to my display. I find that when I zoom in at 110% increments, the bar shrinks until I reach 177% of the default view, where the bar disappears completely. After this point, the bar expands. That's pretty strange.
Eric
On Mar 25, 2010, at 11:59 AM, Bruce Fischl wrote:
Hi Eric,
it doesn't shrink for me, it expands. And I'm pretty sure it's 1cm, not 1mm (which is about the vertex spacing), so the guide must be wrong. We'll fix it
Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
Thanks Bruce. I just checked the TkSurferGuide and noticed that it says the scale bar is 1mm (which looks about right). However, while the scale bar at the default zoom looks fine, I find that it's length behaves strangely (it shrinks) when I zoom into the image. Does the distance value change, or might there be something wrong with my display?
Eric
On Mar 25, 2010, at 11:34 AM, Bruce Fischl wrote:
Hi Eric, in tksurfer click view->scale bar to see the 1cm bar. cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative? Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
Along these same lines, is it possible to overlay/display a Cartesian grid on the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to specify what the 'north pole' of this coordinate system is? For example, if I wanted it to be at the posterior end of the STS. I'm looking to do this on a flat patch. Thanks.
-Derin
On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
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 Derin,
you could try this in tksurfer, but it isn't terribly well documented or supported (or remembered by me). I hacked some stuff together in tksurfer to get those images, but haven't used it in more than 10 years. Do you have the source? You're welcome to poke through it, but I'm not sure it works anymore.
sorry for the unhelpful answer :< Bruce
On Thu, 25 Mar 2010, Derin Cobia wrote:
Along these same lines, is it possible to overlay/display a Cartesian grid on the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to specify what the 'north pole' of this coordinate system is? For example, if I wanted it to be at the posterior end of the STS. I'm looking to do this on a flat patch. Thanks.
-Derin
On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
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.
Don't have the source, but I could download it. What am I looking for? Do you think it would it be possible to do this in Matlab or something, and import in (as an overlay maybe)? New territory for me, I'm sorry too... :(
-Derin
On Mar 25, 2010, at 11:00 AM, Bruce Fischl wrote:
Hi Derin,
you could try this in tksurfer, but it isn't terribly well documented or supported (or remembered by me). I hacked some stuff together in tksurfer to get those images, but haven't used it in more than 10 years. Do you have the source? You're welcome to poke through it, but I'm not sure it works anymore.
sorry for the unhelpful answer :< Bruce
On Thu, 25 Mar 2010, Derin Cobia wrote:
Along these same lines, is it possible to overlay/display a Cartesian grid on the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to specify what the 'north pole' of this coordinate system is? For example, if I wanted it to be at the posterior end of the STS. I'm looking to do this on a flat patch. Thanks.
-Derin
On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
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
sorry Derin, I just poked through the tksurfer source and can't find it. I'll try to look more thoroughly later. I think Mary (Sereno) actually wrote this code to begin with and I modified it, so you could try pinging him On Thu, 25 Mar 2010, Derin Cobia wrote:
Don't have the source, but I could download it. What am I looking for? Do you think it would it be possible to do this in Matlab or something, and import in (as an overlay maybe)? New territory for me, I'm sorry too... :(
-Derin
On Mar 25, 2010, at 11:00 AM, Bruce Fischl wrote:
Hi Derin,
you could try this in tksurfer, but it isn't terribly well documented or supported (or remembered by me). I hacked some stuff together in tksurfer to get those images, but haven't used it in more than 10 years. Do you have the source? You're welcome to poke through it, but I'm not sure it works anymore.
sorry for the unhelpful answer :< Bruce
On Thu, 25 Mar 2010, Derin Cobia wrote:
Along these same lines, is it possible to overlay/display a Cartesian grid on the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to specify what the 'north pole' of this coordinate system is? For example, if I wanted it to be at the posterior end of the STS. I'm looking to do this on a flat patch. Thanks.
-Derin
On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
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
Derin,
You might try importing the surfaces into Caret for this. It seems like there are two needs:
* flat cartesian grid (Menu bar: Layers: Borders: Create Cartesian Flat Analysis Grid Borders (see attached capture) * 3-D scale markers (Toolbar: D/C: Surface Miscellaneous: Surface Cartesian Axes
Here is what the scale markers look like:
http://brainvis.wustl.edu/pub/donna/US/WASHINGTON/200803/views.html login pub password download
Donna
On 03/25/2010 11:19 AM, Bruce Fischl wrote:
sorry Derin, I just poked through the tksurfer source and can't find it. I'll try to look more thoroughly later. I think Mary (Sereno) actually wrote this code to begin with and I modified it, so you could try pinging him On Thu, 25 Mar 2010, Derin Cobia wrote:
Don't have the source, but I could download it. What am I looking for? Do you think it would it be possible to do this in Matlab or something, and import in (as an overlay maybe)? New territory for me, I'm sorry too... :(
-Derin
On Mar 25, 2010, at 11:00 AM, Bruce Fischl wrote:
Hi Derin,
you could try this in tksurfer, but it isn't terribly well documented or supported (or remembered by me). I hacked some stuff together in tksurfer to get those images, but haven't used it in more than 10 years. Do you have the source? You're welcome to poke through it, but I'm not sure it works anymore.
sorry for the unhelpful answer :< Bruce
On Thu, 25 Mar 2010, Derin Cobia wrote:
Along these same lines, is it possible to overlay/display a Cartesian grid on the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to specify what the 'north pole' of this coordinate system is? For example, if I wanted it to be at the posterior end of the STS. I'm looking to do this on a flat patch. Thanks.
-Derin
On Mar 25, 2010, at 10:34 AM, Bruce Fischl wrote:
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers, Bruce On Thu, 25 Mar 2010, Eric Moulton wrote:
I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative?
Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772
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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Donna Dierker -
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