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)
