Package: pySimpleBrainPlot
pySimpleBrainPlotThis package is the python version of matlab package Simple-Brain-Plot contributed by Scholtens, Lianne H, de Lange, Siemon C, and van den Heuvel, Martijn P. The original matlab package can be found at:https://github.com/dutchconnectomelab/Simple-Brain-PlotAtlases availableThis tool can be used to visualize the brain areas in the following atlases:‘Desikan-Killiany’ aparc cortical atlas as present in FreeSurfer [1].‘Desikan-Killiany’ aparc+aseg combined cortical and subcortical atlas as present in FreeSurfer [1].120 regions Cammoun sub-parcellation of the Desikan-Killiany cortical atlas [2].120 regions Cammoun sub-parcellation of the Desikan-Killiany cortical atlas with ASEG subcortical regions [2].250 regions Cammoun sub-parcellation of the Desikan-Killiany atlas [2].39 regions combined Walker-von Bonin and Bailey (WBB47) parcellation atlas of the macaque [3][4][5][6].InstallationThis package now can be installed from PyPI using pip:pipinstallpysimplebrainplotUsageimportnumpyasnpimportpySimpleBrainPlotassbpvalues=np.random.uniform(-1,1,128)sbp.plotBrain('lausanne120_aseg',values)Parametersatlas(str):nameoftheatlastobeused.'aparc'-Desikan-Killianyatlas(68regions)'aparc_aseg'-Desikan-Killianyatlas+subcorticalASEGsegmentation(82regions)'lausanne120'-120regionsCammounsub-parcellationoftheDesikan-Killianyatlas(114regions)'lausanne120_aseg'-120regionsCammounsub-parcellation+subcorticalASEGsegmentation(128regions)'lausanne250'-250regionsCammounsub-parcellation(219regions)'wbb47'-39regionscombinedWalker-vonBoninandBaileyparcellationatlasofthemacaque(39regions)values(array):valuestobeplotted.Shouldbeavectorwiththesamelengthasthenumberofregionsintheatlas.vmin(float):minimumvaluetobeplotted.IfNone,theminimumvalueinthevaluesvectorisused.vmax(float):maximumvaluetobeplotted.IfNone,themaximumvalueinthevaluesvectorisused.save_path(str):pathtosavethesvgfile.save_file(str):prefixofthesvgfile.cm(str):nameofthecolormaptobeused.Shouldbeadefaultmatplotlibcolormap.scaling(float):scalingfactorforthesizeofthesvg.Defaultis0.1.viewer(bool):ifTrue,thesvgisopenedinthedefaultbrowser.DefaultisFalse.Overview of the atlasesReferences[1] Rahul S. Desikan, Florent Ségonne, Bruce Fischl, Brian T. Quinn, Bradford C. Dickerson, Deborah Blacker, Randy L. Buckner, Anders M. Dale, R. Paul Maguire, Bradley T. Hyman, Marilyn S. Albert, and Ronald J. Killiany. An automated labeling system for subdividing the human cerebral cortex on mri scans into gyral based regions of interest. NeuroImage, 31(3):968–80, 2006. URL:http://www.sciencedirect.com/science/article/pii/S1053811906000437, doi:10.1016/j.neuroimage.2006.01.021.[2] Leila Cammoun, Xavier Gigandet, Djalel Meskaldji, Jean Philippe Thiran, Olaf Sporns, Kim Q. Do, Philippe Maeder, Reto Meuli, and Patric Hagmann. Mapping the human connectome at multiple scales with diffusion spectrum mri. Journal of Neuroscience Methods, 203(2):386–397, 2012. doi:10.1016/j.jneumeth.2011.09.031.[3] Lianne H. Scholtens, Ruben Schmidt, Marcel A. de Reus, Martijn P. van den Heuvel. Linking Macroscale Graph Analytical Organization to Microscale Neuroarchitectonics in the Macaque Connectome. Journal of Neuroscience 3 September 2014, 34 (36) 12192-12205; URL:https://www.jneurosci.org/content/34/36/12192.shortDOI: 10.1523/JNEUROSCI.0752-14.2014[4] Stephan KE, Hilgetag CC, Burns GA, O'Neill MA, Young MP, Kötter R. Computational analysis of functional connectivity between areas of primate cerebral cortex. Philos Trans R Soc Lond B Biol Sci 355:111–126, 2000. URL:https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2000.0552doi:10.1098/rstb.2000.0552, pmid:10703047[5] von Bonin G, Bailey P. The neocortex of Macaca mulatta. 1947. University of Illinois, Urbana, IL.[6] Walker EA. A cytoarchitectural study of the prefrontal area of the macaque monkey. J Comp Neurol 73:59–86, 1940. doi:10.1002/cne.900730106[7] Scholtens, Lianne H, de Lange, Siemon C, and van den Heuvel, Martijn P. 2021. “Simple Brain Plot”. Zenodo.https://doi.org/10.5281/zenodo.5346593