INPUT_CSV = "/neurospin/brainomics/2016_deptms/results/Freesurfer/population.csv" OUTPUT = "/neurospin/brainomics/2016_deptms/results/Freesurfer/data" # Read pop csv pop = pd.read_csv(INPUT_CSV) ############################################################################# ## Build mesh template import brainomics.mesh_processing as mesh_utils cor_l, tri_l = mesh_utils.mesh_arrays(os.path.join(TEMPLATE_PATH, "lh.pial.gii")) cor_r, tri_r = mesh_utils.mesh_arrays(os.path.join(TEMPLATE_PATH, "rh.pial.gii")) cor = np.vstack([cor_l, cor_r]) tri_r += cor_l.shape[0] tri = np.vstack([tri_l, tri_r]) mesh_utils.mesh_from_arrays(cor, tri, path=os.path.join(TEMPLATE_PATH, "lrh.pial.gii")) shutil.copyfile(os.path.join(TEMPLATE_PATH, "lrh.pial.gii"), os.path.join(OUTPUT , "lrh.pial.gii")) ############################################################################# # Read images n = len(pop) assert n == 34 Z = np.zeros((n, 2)) #Age,sex y = np.zeros((n, 1)) # DX surfaces = list() for i, ID in enumerate(pop['subject']): cur = pop[pop["subject"] == ID] ics mri_path_lh = cur["mri_path_lh"].values[0] mri_path_rh = cur["mri_path_rh"].values[0]
mesh_perfo__centered = aims.SurfaceGenerator.cylinder(ext1, ext2, 1, 1, 100, 1, 1) """ tri_lacunes_all = np.vstack(tri_lacunes_all) tri_perfo_all = np.vstack(tri_perfo_all) ### ======================================================================= ### mnts_inv_pc12__lacunes__max_inertia_to_yaxis ### ======================================================================= mnts_inv_pc12__lacunes__max_inertia_to_yaxis_scaled_all = \ np.vstack(mnts_inv_pc12__lacunes__max_inertia_to_yaxis_scaled_all) mesh_processing.mesh_from_arrays( mnts_inv_pc12__lacunes__max_inertia_to_yaxis_scaled_all, tri_lacunes_all, path=os.path.join( OUTPUT, "mnts_inv_pc12__lacunes__max_inertia_to_yaxis_scaled.gii")) mnts_inv_pc12__lacunes__max_inertia_to_yaxis_all = \ np.vstack(mnts_inv_pc12__lacunes__max_inertia_to_yaxis_all) mesh_processing.mesh_from_arrays( mnts_inv_pc12__lacunes__max_inertia_to_yaxis_all, tri_lacunes_all, path=os.path.join(OUTPUT, "mnts_inv_pc12__lacunes__max_inertia_to_yaxis.gii")) mnts_inv_pc12__perfo__max_inertia_to_yaxis_all = \ np.vstack(mnts_inv_pc12__perfo__max_inertia_to_yaxis_all) mesh_processing.mesh_from_arrays( mnts_inv_pc12__perfo__max_inertia_to_yaxis_all, tri_perfo_all,