l_labels = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ 'response_dhollander/100408/my_labels/native/native_lh_VMV3.label' r_labels = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ 'response_dhollander/100408/my_labels/native/native_rh_VMV3.label' lr_labels_vir_name = 'native_lrh_VMV3' lr_labels_path = [l_labels, r_labels] labels_values = label2surf_roi(lr_labels_path, geo_path) # surface_streamlines_map(subjects_dir, subject_id, hemi, surf, alpha, labels_values) # # surface_roi_contour(subjects_dir, subject_id, hemi, surf, alpha, lr_label, lr_label) streams = select_by_surf_rois(streamlines, labels_values, geo_path) suffix = [] for i in range(len(lr_labels_path)): suffix.append(os.path.split(lr_labels_path[i])[1].split('.')[-2]) if len(streams) == 3: suffix.append(lr_labels_vir_name) # # print suffix # out_path = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ 'response_dhollander/100408/result/ROIs_fibs/hcp_VanEssen_Atlas/VMV3/%s_fib_SD_stream.tck' for j in range(len(streams)): fasciculus.set_data(streams[j]) fasciculus.save2tck(out_path % suffix[j]) # for i in range(len(streams)): # fiber_simple_3d_show_advanced(img, streams[i], 1)
from pyfat.algorithm.fiber_extract import FibSelection # load data # file = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ # 'response_dhollander/100206/Diffusion/100k_sift_1M45006_dynamic250.tck' file = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ 'response_dhollander/100408/result/result20vs45/Prob01_plenium_fib_vis.tck' fasciculus = Fasciculus(file) # extract CC fibselection = FibSelection(fasciculus) L_temp_need0 = fibselection.endpoint_dissimilarity() fasciculus.set_data(L_temp_need0) L_temp_need1 = fibselection.single_point_mid_sag() fasciculus.set_data(L_temp_need1) L_temp_need2 = fibselection.lr_step() fasciculus.set_data(L_temp_need2) out_path = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ 'response_dhollander/100408/result/result20vs45/Prob01_plenium_fib_vis_pure.tck' fasciculus.save2tck(out_path) # if __name__ == '__main__': # fib_path = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ # 'response_dhollander/100408/result/result20vs45/Prob01_plenium_fib.tck' # out_path = '/home/brain/workingdir/data/dwi/hcp/preprocessed/' \ # 'response_dhollander/100408/result/result20vs45/Prob01_plenium_fib_vis.tck' # fasciculus = Fasciculus(fib_path) # fib = FibSelection(fasciculus) # se = fib.fib_plenium(-78) # fasciculus.set_data(se) # fasciculus.save2tck(out_path)