Hi,
I'd like to show correlation coefficients by region on the brain surface. So for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color each atlas region according to the module it has been assigned to.
It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what.
Thank you! Kx
Hi Kirstie,
You could write your own CLUT file with the color corresponding to the correlation you want to show? Just open up the file and play with the values in the color columns. Then simply load the color table in Freeview and use it to visualize the annotation.
There are of course other ways, but this is probably the quickest.
hth d
On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi,
I'd like to show correlation coefficients by region on the brain surface. So for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color each atlas region according to the module it has been assigned to.
It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what.
Thank you! Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com
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 Kirstie,
Here's an example of how to do this in PySurfer: http://pysurfer.github.io/examples/plot_parc_values.html
Hope that helps, Michael
On Tue, Mar 29, 2016 at 8:08 AM, dgw dgwakeman@gmail.com wrote:
Hi Kirstie,
You could write your own CLUT file with the color corresponding to the correlation you want to show? Just open up the file and play with the values in the color columns. Then simply load the color table in Freeview and use it to visualize the annotation.
There are of course other ways, but this is probably the quickest.
hth d
On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi,
I'd like to show correlation coefficients by region on the brain
surface. So
for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color
each
atlas region according to the module it has been assigned to.
It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what.
Thank you! Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com
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
Thank you Michael! I <3 Pysurfer.
(and freesurfer of course!)
The *real* goal is to integrate the code that I've written as a wrapper around pysurfer to show regional values (exactly as you suggest) with BrainNet https://www.nitrc.org/projects/bnv/ which can show the network nicely on top of freesurfer files.
Here's the wiki for my pysurfer wrapper: https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-wit...
And the code itself https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFA...
Unfortunately I don't use BrainNet so I'm having difficulty helping my lab mate make his pretty plots of network nodes and edges overlayed on top of surface colors (eg: modular partition)!
Is there a way of writing out an annot file from pysurfer into freesurfer format? Maybe that would bring the two packages closer together....
Kx
On 29 March 2016 at 16:29, Michael Waskom mwaskom@stanford.edu wrote:
Hi Kirstie,
Here's an example of how to do this in PySurfer: http://pysurfer.github.io/examples/plot_parc_values.html
Hope that helps, Michael
On Tue, Mar 29, 2016 at 8:08 AM, dgw dgwakeman@gmail.com wrote:
Hi Kirstie,
You could write your own CLUT file with the color corresponding to the correlation you want to show? Just open up the file and play with the values in the color columns. Then simply load the color table in Freeview and use it to visualize the annotation.
There are of course other ways, but this is probably the quickest.
hth d
On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi,
I'd like to show correlation coefficients by region on the brain
surface. So
for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color
each
atlas region according to the module it has been assigned to.
It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what.
Thank you! Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com
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
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 Kirstie,
Nibabel has a write_annot function that should work: http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfe...
Best, Michael
On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Thank you Michael! I <3 Pysurfer.
(and freesurfer of course!)
The *real* goal is to integrate the code that I've written as a wrapper around pysurfer to show regional values (exactly as you suggest) with BrainNet https://www.nitrc.org/projects/bnv/ which can show the network nicely on top of freesurfer files.
Here's the wiki for my pysurfer wrapper: https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-wit...
And the code itself https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFA...
Unfortunately I don't use BrainNet so I'm having difficulty helping my lab mate make his pretty plots of network nodes and edges overlayed on top of surface colors (eg: modular partition)!
Is there a way of writing out an annot file from pysurfer into freesurfer format? Maybe that would bring the two packages closer together....
Kx
On 29 March 2016 at 16:29, Michael Waskom mwaskom@stanford.edu wrote:
Hi Kirstie,
Here's an example of how to do this in PySurfer: http://pysurfer.github.io/examples/plot_parc_values.html
Hope that helps, Michael
On Tue, Mar 29, 2016 at 8:08 AM, dgw dgwakeman@gmail.com wrote:
Hi Kirstie,
You could write your own CLUT file with the color corresponding to the correlation you want to show? Just open up the file and play with the values in the color columns. Then simply load the color table in Freeview and use it to visualize the annotation.
There are of course other ways, but this is probably the quickest.
hth d
On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi,
I'd like to show correlation coefficients by region on the brain
surface. So
for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color
each
atlas region according to the module it has been assigned to.
It seems like I have to do something with the ?h.aparc.annot files and
a
colour lookup table but I'm not sure exactly what.
Thank you! Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com
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
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.
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
*Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
*Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com
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.
Brilliant - I think that's probably my friend!
Thanks again everyone for all the help! Kx
On 29 March 2016 at 16:50, Michael Waskom mwaskom@stanford.edu wrote:
Hi Kirstie,
Nibabel has a write_annot function that should work: http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfe...
Best, Michael
On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Thank you Michael! I <3 Pysurfer.
(and freesurfer of course!)
The *real* goal is to integrate the code that I've written as a wrapper around pysurfer to show regional values (exactly as you suggest) with BrainNet https://www.nitrc.org/projects/bnv/ which can show the network nicely on top of freesurfer files.
Here's the wiki for my pysurfer wrapper: https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-wit...
And the code itself https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFA...
Unfortunately I don't use BrainNet so I'm having difficulty helping my lab mate make his pretty plots of network nodes and edges overlayed on top of surface colors (eg: modular partition)!
Is there a way of writing out an annot file from pysurfer into freesurfer format? Maybe that would bring the two packages closer together....
Kx
On 29 March 2016 at 16:29, Michael Waskom mwaskom@stanford.edu wrote:
Hi Kirstie,
Here's an example of how to do this in PySurfer: http://pysurfer.github.io/examples/plot_parc_values.html
Hope that helps, Michael
On Tue, Mar 29, 2016 at 8:08 AM, dgw dgwakeman@gmail.com wrote:
Hi Kirstie,
You could write your own CLUT file with the color corresponding to the correlation you want to show? Just open up the file and play with the values in the color columns. Then simply load the color table in Freeview and use it to visualize the annotation.
There are of course other ways, but this is probably the quickest.
hth d
On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker kw401@cam.ac.uk wrote:
Hi,
I'd like to show correlation coefficients by region on the brain
surface. So
for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to
color each
atlas region according to the module it has been assigned to.
It seems like I have to do something with the ?h.aparc.annot files
and a
colour lookup table but I'm not sure exactly what.
Thank you! Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com
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
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.
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
*Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
*Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com
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
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
-
dgw -
Kirstie Whitaker -
Michael Waskom