Network analyses for fMRI

Talk from the 23 & 24 January 2012 "GlaxoSmithKline - Neurophysics Workshop on Pharmacological MRI", an activity hosted at Warwick University and coordinated with the Neurophysics Marie Curie Initial Training Network of which GSK is a participant

Vertes2016_PhilTransB_data.mat

<p>This dataset contains all fMRI (and related) data needed to replicate analyses in the referenced paper.</p><p><br></p><p>The file is in MATLAB .mat format and contains the following variables:</p><p><br></p> <p><b>ROI_mni:</b> the x, y, z coordinates in MNI space for all 308 initial regions of interest – these are the coordinates used for matching to the Allen Institute for Brain Science gene expression data.</p> <p> </p> <p><b>names:</b> the anatomical labels for all 308 initial regions of interest</p> <p> </p> <p><b>vonEconomo: </b>a vector containing the cytoarchitectonic class assigned to each of the 308 cortical regions of interest. Classes are numbered 1 to 7, in the same order as defined in Figure 1 of the main text.</p> <p><br></p> <p><b>excluded_ROI_fmri:</b> a binary vector containing one entry per region of interest (308x1).  The 21 regions which were excluded from further analysis due to fMRI dropout have value =1, all other regions have value = 0.</p> <p> </p> <p><b>Co:</b> contains the 38 fully weighted 287x287 connectivity matrices for all 38 usable subjects and all 287 usable regions of interest.</p> <p><br></p> <p><b>Com:</b> the modular assignment of all 287 usable regions based on consensus modular partition of the group average correlation matrix at 10% connection density.</p> <p><br></p> <p><b>meas: </b>a structure containing nodal network metrics for all 287 usable MRI regions of interest. The measures included are: degree (meas.k), inter-modular degree (meas.Inter_k), intra-modular degree (meas.Intra_k), participation coefficient (meas.PC) and average nodal distance (meas.d).</p> <p> </p> <p><b>excluded_ROI_genes: </b>a binary vector containing one entry per region of interest (308x1).  The 2 regions which were excluded from PLS analyses due to outlier gene data have value =1, all other regions have value = 0.</p><p><br></p><div><div><div> </div> </div> </div

MAGICC vertex-level gene expression data

Vertex-level expression data from the Multiscale Atlas of Gene Expression for Integrative Cortical CartographyFiles include:Template cortical surface meshes for flat, inflated and very_inflated surfaces with 32k verticesfs_LR.32k.L.flat.surf.giifs_LR.32k.L.inflated.surf.giifs_LR.32k.L.very_inflated.surf.giiGlasser_2016.32k.L.label.gii - parcellation of fs_LR 32k surface according to Glasser et al., 2016 Nature.ahba_vertex.npy - Atlas of cortical gene expression for 20,781 genes at 32k vertex locationsahba_vertex_gradients.npy - Atlas of cortical gene expression gradients for 20,781 genes at 32k vertex locationsSuppTable2.csv - Gene-level characterisations for 20,781 in the same order as the above files. Includes gene symbol, alongside many other annotations described in the manuscript.Example to code to analyse these data can be found at:https://github.com/kwagstyl/magicc</p