def volstats (invol, groupname, groupsize, outdir=''): slicesdir = os.path.dirname(invol) if not outdir: outdir = slicesdir base = os.path.basename(au.remove_ext(invol)) outmeanf = outdir + os.path.sep + base + '_' + au.mean_str() outvarf = outdir + os.path.sep + base + '_' + au.var_str() outstdf = outdir + os.path.sep + base + '_' + au.std_str() outsumsf = outdir + os.path.sep + base + '_' + au.sums_str() vol = nib.load(invol).get_data() aff = nib.load(invol).get_affine() if not os.path.exists(outmeanf): mean = np.mean(vol, axis=3) au.save_nibabel(outmeanf, mean, aff) if not os.path.exists(outstdf): std = np.std(vol, axis=3) au.save_nibabel(outstdf, std, aff) if not os.path.exists(outvarf): var = np.var(vol, axis=3) au.save_nibabel(outvarf, var, aff) if not os.path.exists(outsumsf): sums = np.sum(vol, axis=3) au.save_nibabel(outsumsf, sums, aff) return [outsumsf,outmeanf,outvarf,outstdf]
def volstats(invol, groupname, groupsize, outdir=''): slicesdir = os.path.dirname(invol) if not outdir: outdir = slicesdir base = os.path.basename(au.remove_ext(invol)) outmeanf = outdir + os.path.sep + base + '_' + au.mean_str() outvarf = outdir + os.path.sep + base + '_' + au.var_str() outstdf = outdir + os.path.sep + base + '_' + au.std_str() outsumsf = outdir + os.path.sep + base + '_' + au.sums_str() vol = nib.load(invol).get_data() aff = nib.load(invol).get_affine() if not os.path.exists(outmeanf): mean = np.mean(vol, axis=3) au.save_nibabel(outmeanf, mean, aff) if not os.path.exists(outstdf): std = np.std(vol, axis=3) au.save_nibabel(outstdf, std, aff) if not os.path.exists(outvarf): var = np.var(vol, axis=3) au.save_nibabel(outvarf, var, aff) if not os.path.exists(outsumsf): sums = np.sum(vol, axis=3) au.save_nibabel(outsumsf, sums, aff) return [outsumsf, outmeanf, outvarf, outstdf]
def get_stats_fnames (groupnames, outdir=''): if np.ndim(groupnames) == 0: groupnames = [groupnames] if outdir: outdir += outdir + os.path.sep mnames = [au.sums_str(), au.mean_str(), au.var_str(), au.std_str()] ngroups = len(groupnames) statfnames = np.zeros ([ngroups, len(mnames)], dtype=np.dtype('a2000')) for g in np.arange(ngroups): group = groupnames[g] for m in np.arange(len(mnames)): measure = mnames[m] statfnames[g,m] = outdir + group + '_' + measure + au.ext_str() return [statfnames, mnames]
def get_stats_fnames(groupnames, outdir=''): if np.ndim(groupnames) == 0: groupnames = [groupnames] if outdir: outdir += outdir + os.path.sep mnames = [au.sums_str(), au.mean_str(), au.var_str(), au.std_str()] ngroups = len(groupnames) statfnames = np.zeros([ngroups, len(mnames)], dtype=np.dtype('a2000')) for g in np.arange(ngroups): group = groupnames[g] for m in np.arange(len(mnames)): measure = mnames[m] statfnames[g, m] = outdir + group + '_' + measure + au.ext_str() return [statfnames, mnames]