sct.run('sct_compute_hausdorff_distance.py -i ' + res_gm_seg_bin.file_name + ext + ' -r ' + im_ref_gm_seg.file_name + ext + ' -t 1 -o ' + hd_name + ' -v ' + str(self.param.verbose)) sct.run('mv ./' + hd_name + ' ../../') os.chdir('..') return dice_name, hd_name ######################################################################################################################## # ------------------------------------------------------ MAIN ------------------------------------------------------- # ######################################################################################################################## if __name__ == "__main__": param = Param() input_target_fname = None input_sc_seg_fname = None input_t2_data = None input_level_fname = None input_ref_gm_seg = None if param.debug: print '\n*** WARNING: DEBUG MODE ON ***\n' fname_input = param.path_dictionary + "/errsm_34.nii.gz" fname_input = param.path_dictionary + "/errsm_34_seg_in.nii.gz" else: param_default = Param() # Initialize the parser parser = Parser(__file__) parser.usage.set_description(
dice_fic.close() # sct.run(' mv ./' + dice_name + ' ../') return dice_name ######################################################################################################################## # ------------------------------------------------------ MAIN ------------------------------------------------------- # ######################################################################################################################## if __name__ == "__main__": param = Param() input_target_fname = None input_sc_seg_fname = None input_t2_data = None input_level_fname = None input_ref_gm_seg = None if param.debug: print '\n*** WARNING: DEBUG MODE ON ***\n' fname_input = param.path_dictionary + "/errsm_34.nii.gz" fname_input = param.path_dictionary + "/errsm_34_seg_in.nii.gz" else: param_default = Param() # Initialize the parser parser = Parser(__file__) parser.usage.set_description('Project all the input image slices on a PCA generated from set of t2star images')
dice_fic.write( "\n\n--------------------------------------------------------------\nDice coefficient on the White Matter segmentation:\n" ) dice_fic.write(output_wm) dice_fic.close() # sct.run(' mv ./' + dice_name + ' ../') return dice_name ######################################################################################################################## # ------------------------------------------------------ MAIN ------------------------------------------------------- # ######################################################################################################################## if __name__ == "__main__": param = Param() input_target_fname = None input_sc_seg_fname = None input_t2_data = None input_level_fname = None input_ref_gm_seg = None if param.debug: print "\n*** WARNING: DEBUG MODE ON ***\n" fname_input = param.path_dictionary + "/errsm_34.nii.gz" fname_input = param.path_dictionary + "/errsm_34_seg_in.nii.gz" else: param_default = Param() # Initialize the parser parser = Parser(__file__) parser.usage.set_description("Project all the input image slices on a PCA generated from set of t2star images")
# sct.run(' mv ./' + dice_name + ' ../') hd_name = 'hd_' + sct.extract_fname(self.target_fname)[1] + '_' + self.param.res_type + '.txt' sct.run('sct_compute_hausdorff_distance.py -i ' + res_gm_seg_bin.file_name + ext + ' -r ' + im_ref_gm_seg.file_name + ext + ' -t 1 -o ' + hd_name + ' -v ' + str(self.param.verbose)) sct.run('mv ./' + hd_name + ' ../../') os.chdir('..') return dice_name, hd_name ######################################################################################################################## # ------------------------------------------------------ MAIN ------------------------------------------------------- # ######################################################################################################################## if __name__ == "__main__": param = Param() input_target_fname = None input_sc_seg_fname = None input_t2_data = None input_level_fname = None input_ref_gm_seg = None if param.debug: print '\n*** WARNING: DEBUG MODE ON ***\n' fname_input = param.path_dictionary + "/errsm_34.nii.gz" fname_input = param.path_dictionary + "/errsm_34_seg_in.nii.gz" else: param_default = Param() # Initialize the parser parser = Parser(__file__) parser.usage.set_description('Project all the input image slices on a PCA generated from set of t2star images')