# Output prefixes obase = "/home2/data/Projects/CWAS/figures" odir = path.join(obase, "fig_03") if not path.exists(odir): os.mkdir(odir) ### ### # Get scan overlays # Scan 1 i = 0 print pfiles[i] sw1 = SurfWrap() sw1.set_overlay("overlap", pfiles[i], "red-yellow") scan1_lh = io.read_scalar_data(sw1.overlay_surf['lh']) scan1_rh = io.read_scalar_data(sw1.overlay_surf['rh']) # Scan 2 i = 1 print pfiles[i] sw2 = SurfWrap() sw2.set_overlay("overlap", pfiles[i], "red-yellow") scan2_lh = io.read_scalar_data(sw2.overlay_surf['lh']) scan2_rh = io.read_scalar_data(sw2.overlay_surf['rh']) ### ### # Get minimum and maximum values across the two scans
data_min = data_max else: data_min = data[data.nonzero()].min() return [data_min, data_max] print "...loop through scans" for i,scan in enumerate(scans): ### # Get individual percentile maps print "individual data maps" # MDMR w/o mdmr1_lh = io.read_scalar_data(sfiles1[scan]['lh']) mdmr1_rh = io.read_scalar_data(sfiles1[scan]['rh']) # MDMR w/ mdmr2_lh = io.read_scalar_data(sfiles2[scan]['lh']) mdmr2_rh = io.read_scalar_data(sfiles2[scan]['rh']) ### ### # Create overlap print "creating and saving overlap" # Threshold MDMR w/o global
obase = "/home2/data/Projects/CWAS/figures" odir = path.join(obase, "fig_03") if not path.exists(odir): os.mkdir(odir) ### ### # Get scan overlays # Scan 1 i = 0 print pfiles[i] sw1 = SurfWrap() sw1.set_overlay("overlap", pfiles[i], "red-yellow") scan1_lh = io.read_scalar_data(sw1.overlay_surf['lh']) scan1_rh = io.read_scalar_data(sw1.overlay_surf['rh']) # Scan 2 i = 1 print pfiles[i] sw2 = SurfWrap() sw2.set_overlay("overlap", pfiles[i], "red-yellow") scan2_lh = io.read_scalar_data(sw2.overlay_surf['lh']) scan2_rh = io.read_scalar_data(sw2.overlay_surf['rh']) ### ### # Get minimum and maximum values across the two scans
### ### # Read in data for i in range(2): print "scan: %s" % scans[i] print "read data" cwas_info = vol_to_surf(pfiles[i], hemis=["lh", "rh"]) lh_cwas = io.read_scalar_data(cwas_info["lh"]) rh_cwas = io.read_scalar_data(cwas_info["rh"]) glm_info = vol_to_surf(gfiles[i], hemis=["lh", "rh"]) lh_glm = io.read_scalar_data(glm_info["lh"]) rh_glm = io.read_scalar_data(glm_info["rh"]) ### ### # Remap with top percentiles print "percentiles" # Top 5%, 10%, & 15%
data_min = data_max else: data_min = data[data.nonzero()].min() return [data_min, data_max] print "...loop through scans" for i, scan in enumerate(scans): ### # Get individual percentile maps print "individual data maps" # MDMR w/o mdmr1_lh = io.read_scalar_data(sfiles1[scan]['lh']) mdmr1_rh = io.read_scalar_data(sfiles1[scan]['rh']) # MDMR w/ mdmr2_lh = io.read_scalar_data(sfiles2[scan]['lh']) mdmr2_rh = io.read_scalar_data(sfiles2[scan]['rh']) ### ### # Create overlap print "creating and saving overlap" # Threshold MDMR w/o global mdmr1_lh[mdmr1_lh.nonzero()] = 1
odir = path.join(obase, "fig_03") if not path.exists(odir): os.mkdir(odir) ### ### # Get scan overlays # Scan 1 i = 0 print pfiles[i] sw1 = SurfWrap() sw1.set_overlay("overlap", pfiles[i], "red-yellow") scan1_lh = io.read_scalar_data(sw1.overlay_surf["lh"]) scan1_rh = io.read_scalar_data(sw1.overlay_surf["rh"]) # Scan 2 i = 1 print pfiles[i] sw2 = SurfWrap() sw2.set_overlay("overlap", pfiles[i], "red-yellow") scan2_lh = io.read_scalar_data(sw2.overlay_surf["lh"]) scan2_rh = io.read_scalar_data(sw2.overlay_surf["rh"]) ### ### # Get minimum and maximum values across the two scans