Hi Kirstie, Nibabel has a write_annot function that should work: http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#write-annot
Best, Michael On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker <kw...@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-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 > > _______________________________________________ > 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. > >
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