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 <mwas...@stanford.edu> wrote: > 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. >> >> > > _______________________________________________ > 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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