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-with-Pysurfer And the code itself https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py 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 <mwas...@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 <dgwake...@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 <kw...@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
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