code_path = os.path.join(base_path, "code")
log_path = os.path.join(code_path, "log")
preprocess_data_path = os.path.join(base_path, "preprocess_data")
# path to the Makefile
make_file_path = os.path.join(code_path, "Makefile")
# path to where to save the post-flirt nii
AD_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "AD")
Normal_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt",
"Normal")
PD_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "PD")
# get nii paths for subject unique
AD_nii_files = process_nii.get_nii(AD_afterflirt_path)
(unique_AD_subj, unique_AD_nii_files) = go_array.unique_sub_files(AD_nii_files)
Normal_nii_files = process_nii.get_nii(Normal_afterflirt_path)
(unique_Normal_subj,
unique_Normal_nii_files) = go_array.unique_sub_files(Normal_nii_files)
PD_nii_files = process_nii.get_nii(PD_afterflirt_path)
(unique_PD_subj, unique_PD_nii_files) = go_array.unique_sub_files(PD_nii_files)
unique_data_dict = {
"AD": unique_AD_nii_files,
"Normal": unique_Normal_nii_files,
"PD": unique_PD_nii_files
}
############ functions to get randomized train valid test
AD_skullstrip_path = os.path.join(preprocess_data_path, "skull_strip", "AD")
Normal_skullstrip_path = os.path.join(preprocess_data_path, "skull_strip", "Normal")
PD_skullstrip_path = os.path.join(preprocess_data_path, "skull_strip", "PD")
# path to where to save the post-flirt nii
AD_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "AD")
Normal_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "Normal")
PD_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "PD")
AD_afterfnirt_path = os.path.join(preprocess_data_path, "after_fnirt", "AD")
Normal_afterfnirt_path = os.path.join(preprocess_data_path, "after_fnirt", "Normal")
PD_afterfnirt_path = os.path.join(preprocess_data_path, "after_fnirt", "PD")
# visualize raw data
AD1 = process_nii.get_nii(AD_raw_data_path)
Normal1 = process_nii.get_nii(Normal_raw_data_path)
PD1 = process_nii.get_nii(PD_raw_data_path)
my_dict = {"AD":AD1, "PD":PD1, "Normal": Normal1}
process_nii.random_visualization(5, my_dict, "raw_data")
# visualize reoriented data
AD1_reorient = process_nii.get_nii(AD_fixorient_path)
Normal1_reorient = process_nii.get_nii(Normal_fixorient_path)
PD1_reorient = process_nii.get_nii(PD_fixorient_path)
my_dict_reorient = {"AD":AD1_reorient, "PD": PD1_reorient, "Normal": Normal1_reorient}
process_nii.random_visualization(5, my_dict_reorient, "test_reorient")
# visualize skull stripped data
base_path = os.path.join(base_path, "..")
raw_data_path = os.path.join(base_path, "raw_data")
code_path = os.path.join(base_path, "code")
log_path = os.path.join(code_path, "log")
preprocess_data_path = os.path.join(base_path, "preprocess_data")
# path to the Makefile
make_file_path = os.path.join(code_path, "Makefile")
# path to where to save the post-flirt nii
AD_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "AD")
Normal_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt",
"Normal")
PD_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "PD")
# Bad files
Bad_afterflirt_path = os.path.join(preprocess_data_path, "after_flirt", "Bad")
Bad_to_h5 = os.path.join(preprocess_data_path, "Real_bad_matrix.h5")
# get nii paths for bad data
# convert to subjects x 1d array
Bad_nii_files = process_nii.get_nii(Bad_afterflirt_path)
bad_matrix = go_array.nii_to_1d_simple(Bad_nii_files,
Bad_to_h5,
normalization=True,
smooth=1,
tf=False)
print(bad_matrix.shape)
print(bad_matrix.dtype)