else: data_min = data[data.nonzero()].min() return [data_min, data_max] print 'getting range' ranges = np.array([get_range(pfile) for pfile in pfiles]) dmin = ranges.min() dmax = ranges.max() print 'min=%.4f; max=%.4f' % (dmin, dmax) ### ### # Surface Viz for i, pfile in enumerate(pfiles): print pfile oprefix = path.join(odir, "C4_fstats_global_easythresh_surface_scan%i" % (i + 1)) sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow", outprefix=oprefix) sw.min = dmin sw.max = dmax sw.run(compilation="box") sw.montage(compilation="stick") ###
] # 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']) ### ###
# 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']) ###
data_max = data.max() if data_max == 0: data_min = data_max else: data_min = data[data.nonzero()].min() return [data_min, data_max] print "getting range" ranges = np.array([get_range(pfile) for pfile in pfiles]) dmin = ranges[ranges != 0].min() dmax = ranges[ranges != 0].max() print "min=%.4f; max=%.4f" % (dmin, dmax) ### ### # Surface Viz for i, pfile in enumerate(pfiles): print pfile oprefix = path.join(odir, "C2_global_perms_surface_scan%i" % (i + 1)) sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow", outprefix=oprefix) sw.min = dmin sw.max = dmax sw.run(compilation="box") sw.montage(compilation="stick") ###
from os import path from surfwrap import SurfWrap obase = "/home2/data/Projects/CWAS/adhd200_rerun/cwas" comparisons = ["adhdc_vs_adhdi", "tdc_vs_adhdc", "tdc_vs_adhdi"] # GLOBAL! preproc = "global" for comparison in comparisons: print "group comparison: %s" % comparison # Input pfile distdir = path.join(obase, "%s_rois_random_k3200" % preproc) mdmrdir = path.join(distdir, "%s_gender+age+iq+mean_FD.mdmr" % comparison) pfile = path.join(mdmrdir, "log_pvals_%s.nii.gz" % comparison) # Output oprefix odir = path.join(mdmrdir, "images") if not path.exists(odir): os.mkdir(odir) oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", "")) # Surface Viz sw = SurfWrap(name=comparison, infile=pfile, cbar="red-yellow", outprefix=oprefix) sw.min = 1.3 sw.run() # import pysurfer # pysurfer = reload(pysurfer) # SurfWrap = pysurfer.SurfWrap
# Input Directory indir = path.join(basedir, "%s_%s" % (strategy, kstr)) # Input Measure Files infiles = [path.join(indir, "%s.nii.gz" % measure) for measure in measures] if not path.exists(infiles[0]): raise Exception("infiles %s doesn't exist" % infiles[0]) # Output prefixes obase = "/home2/data/Projects/CWAS/figures" odir = path.join(obase, "fig_02") if not path.exists(odir): os.mkdir(odir) ### ### # Surface Viz for i, infile in enumerate(infiles): print "%i: %s" % (i, infile) oprefix = path.join(odir, "A_surface_%s" % measures[i]) sw = SurfWrap(name=measures[i], infile=infile, cbar="spectral-cb", outprefix=oprefix) sw.run(compilation="box") sw.montage(compilation="stick") print '' ###
rh_glm_perc += (rh_glm > p) * 1 # Overlap top 15% between mdmr and glm lh_overlap = (lh_cwas_perc>0)*1 + (lh_glm_perc>0)*2 rh_overlap = (rh_cwas_perc>0)*1 + (rh_glm_perc>0)*2 ### ### # Plot top percentiles print "plot percentiles" sw0 = SurfWrap(hemis=['lh']) sw0.set_underlay() sw0.set_options() sw0.min = 1; sw0.max = 3; sw0.sign = "pos" oprefix = op.join(figdir, "B_surface_percentiles") sw0.set_output(oprefix) cwas_perc_surfs = {"lh": lh_cwas_perc} glm_perc_surfs = {"lh": lh_glm_perc} overlap_surfs = {"lh": lh_overlap} for hemi in sw0.hemis: print "visualize %s" % hemi ## MDMR #oprefix = op.join(figdir, "B_%s_percentiles_mdmr" % scans[i])
# Input Directory indir = path.join(basedir, "%s_%s" % (strategy, kstr)) # Input Measure Files infiles = [ path.join(indir, "%s.nii.gz" % measure) for measure in measures ] if not path.exists(infiles[0]): raise Exception("infiles %s doesn't exist" % infiles[0]) # Output prefixes obase = "/home2/data/Projects/CWAS/figures" odir = path.join(obase, "fig_02") if not path.exists(odir): os.mkdir(odir) ### ### # Surface Viz for i,infile in enumerate(infiles): print "%i: %s" % (i,infile) oprefix = path.join(odir, "A_surface_%s" % measures[i]) sw = SurfWrap(name=measures[i], infile=infile, cbar="spectral-cb", outprefix=oprefix) sw.run(compilation="box") sw.montage(compilation="stick") print '' ###
obase = "/home2/data/Projects/CWAS/adhd200_rerun/cwas" comparisons = ["adhdc_vs_adhdi", "tdc_vs_adhdc", "tdc_vs_adhdi"] # GLOBAL! preproc = "global" for comparison in comparisons: print "group comparison: %s" % comparison # Input pfile distdir = path.join(obase, "%s_rois_random_k3200" % preproc) mdmrdir = path.join(distdir, "%s_gender+age+iq+mean_FD.mdmr" % comparison) pfile = path.join(mdmrdir, "log_pvals_%s.nii.gz" % comparison) # Output oprefix odir = path.join(mdmrdir, "images") if not path.exists(odir): os.mkdir(odir) oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", "")) # Surface Viz sw = SurfWrap(name=comparison, infile=pfile, cbar="red-yellow", outprefix=oprefix) sw.min = 1.3 sw.run() # import pysurfer # pysurfer = reload(pysurfer) # SurfWrap = pysurfer.SurfWrap
if name == "vox2vox": dirname = "%s_k%s_to_k%s" % (strategy, k, k) elif name == "roi2vox": dirname = "%s_rois_random_k%04i" % (strategy, k) elif name == "roi2roi": dirname = "%s_only_rois_random_k%04i" % (strategy, k) else: raise Exception("whoops") distdir = path.join(basedir, scan, dirname) # Input pfile mdmrdir = path.join(distdir, mname) pfile = path.join(mdmrdir, cname, "clust_logp_%s.nii.gz" % factor) # Output oprefix odir = path.join(mdmrdir, cname, "images") if not path.exists(odir): os.mkdir(odir) oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", "")) # Surface Viz sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow", outprefix=oprefix) sw.run(compilation="box") # import pysurfer # pysurfer = reload(pysurfer) # SurfWrap = pysurfer.SurfWrap
dirname = "%s_k%s_to_k%s" % (strategy, k, k) elif name == "roi2vox": dirname = "%s_rois_random_k%04i" % (strategy, k) elif name == "roi2roi": dirname = "%s_only_rois_random_k%04i" % (strategy, k) else: raise Exception("whoops") distdir = path.join(basedir, scan, dirname) # Input pfile mdmrdir = path.join(distdir, mname) pfile = path.join(mdmrdir, cname, "clust_logp_%s.nii.gz" % factor) # Output oprefix odir = path.join(mdmrdir, cname, "images") if not path.exists(odir): os.mkdir(odir) oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", "")) # Surface Viz sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow", outprefix=oprefix) sw.run(compilation="box") # import pysurfer # pysurfer = reload(pysurfer) # SurfWrap = pysurfer.SurfWrap