# Compute Hausdorff distance
        hd_name = 'hd_' + sct.extract_fname(self.target_fname)[1] + '_' + self.seg_param.res_type + '.txt'
        sct.run('sct_compute_hausdorff_distance -i '+gm_seg+' -d '+ref_gmseg+' -thinning 1 -o '+hd_name+' -v '+str(self.seg_param.verbose))
        sct.run('mv ./' + hd_name + ' ../')

        os.chdir('..')
        return dice_name, hd_name


########################################################################################################################
# ------------------------------------------------------  MAIN ------------------------------------------------------- #
########################################################################################################################
if __name__ == "__main__":
    model_param = ModelParam()
    seg_param = SegmentationParam()
    input_target_fname = None
    input_sc_seg_fname = None
    input_t2_data = None
    input_level_fname = None
    input_ref_gm_seg = None
    compute_ratio = False
    if seg_param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
        fname_input = model_param.path_model + "/errsm_34.nii.gz"
        fname_input = model_param.path_model + "/errsm_34_seg_in.nii.gz"
    else:
        parser = get_parser()
        arguments = parser.parse(sys.argv[1:])
        input_target_fname = arguments["-i"]
        input_sc_seg_fname = arguments["-s"]
Пример #2
0
    sct.printv('Done!\n'
               'You can warp the template to the target using the following command lines:\n'
               'sct_concat_transfo -w '+multimodal_reg_param.warp_template2anat+','+warp_anat2target_corrected+' -d '+multimodal_reg_param.target+' -o warp_template2'+sct.extract_fname(multimodal_reg_param.target)[1]+'.nii.gz\n'
               'sct_warp_template -d '+multimodal_reg_param.target+' -w warp_template2'+sct.extract_fname(multimodal_reg_param.target)[1]+'.nii.gz', verbose, 'info')
    os.chdir('..')

    if remove:
        sct.printv('\nRemove temporary files...', verbose, 'normal')
        sct.run("rm -rf "+path_tmp)



if __name__ == "__main__":
    multimodal_reg_param = MultimodalRegistrationParam()
    wm_reg_param = WmRegistrationParam()
    gm_seg_param = SegmentationParam()
    remove = True
    verbose = 1

    if wm_reg_param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
    else:
        param_default = WmRegistrationParam()

        # Initialize the parser
        parser = Parser(__file__)
        parser.usage.set_description('Register the template on an image with a white/gray matter contrast according to the internal structure:\n'
                                     ' - register multimodal of the template to the target image\n'
                                     ' - automatic segmentation of the white and gray matter in the target image\n'
                                     ' - correction of the registration of the template to the target according to the WM/GM segmentation')  # TODO: change description
        parser.usage.addSection('General parameters')
    sct.run('cp warp_wm_gm2template2anat* ../'+sct.extract_fname(reg_param.wm_gm2template2anat_warp)[1]+'_wm.nii.gz')

    os.chdir('..')

    sct.printv('Done!\n You can apply the following commands to correct the registration of the template to :\n'
               'sct_concat_transfo -w ../t2/warp_template2anat.nii.gz,'+sct.extract_fname(reg_param.wm_gm2template2anat_warp)[1]+'_wm.nii.gz  -d '+target_fname+' -o warp_template2t2star_with_wm.nii.gz\n'
               ' sct_warp_template -d '+target_fname+' -w warp_template2t2star_with_wm.nii.gz', verbose, 'info')
    # remove temporary file
    if reg_param.remove_temp == 1:
        sct.printv('\nRemove temporary files...', verbose, 'normal')
        sct.run("rm -rf "+path_tmp)


if __name__ == "__main__":
    reg_param = RegistrationParam()
    gm_seg_param = SegmentationParam()
    input_target_fname = ''
    input_sc_seg_fname = ''
    path_to_label = ''

    if reg_param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
    else:
        param_default = RegistrationParam()

        # Initialize the parser
        parser = Parser(__file__)
        parser.usage.set_description('Register the template on a gray matter segmentation')  # TODO: change description
        parser.usage.addSection('Segmentation parameters')
        parser.add_option(name="-i",
                          type_value="file",
        'Done!\n You can apply the following commands to correct the registration of the template to :\n'
        'sct_concat_transfo -w ../t2/warp_template2anat.nii.gz,' +
        sct.extract_fname(reg_param.wm_gm2template2anat_warp)[1] +
        '_wm.nii.gz  -d ' + target_fname +
        ' -o warp_template2t2star_with_wm.nii.gz\n'
        ' sct_warp_template -d ' + target_fname +
        ' -w warp_template2t2star_with_wm.nii.gz', verbose, 'info')
    # remove temporary file
    if reg_param.remove_temp == 1:
        sct.printv('\nRemove temporary files...', verbose, 'normal')
        sct.run("rm -rf " + path_tmp)


if __name__ == "__main__":
    reg_param = RegistrationParam()
    gm_seg_param = SegmentationParam()
    input_target_fname = ''
    input_sc_seg_fname = ''
    path_to_label = ''

    if reg_param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
    else:
        param_default = RegistrationParam()

        # Initialize the parser
        parser = Parser(__file__)
        parser.usage.set_description(
            'Register the template on a gray matter segmentation'
        )  # TODO: change description
        parser.usage.addSection('Segmentation parameters')