Esempio n. 1
0
def main():

    # Initialization
    fname_output = ''
    fname_mask = param.fname_mask
    fname_src_seg = ''
    fsloutput = 'export FSLOUTPUTTYPE=NIFTI; '  # for faster processing, all outputs are in NIFTI'

    start_time = time.time()
    # get path of the toolbox
    status, path_sct = commands.getstatusoutput('echo $SCT_DIR')

    # get default registration parameters
    # step1 = Paramreg(step='1', type='im', algo='syn', metric='MI', iter='5', shrink='1', smooth='0', gradStep='0.5')
    step0 = Paramreg(step='0',
                     type='im',
                     algo='syn',
                     metric='MI',
                     iter='0',
                     shrink='1',
                     smooth='0',
                     gradStep='0.5')  # only used to put src into dest space
    step1 = Paramreg()
    paramreg = ParamregMultiStep([step0, step1])

    # Initialize the parser
    parser = Parser(__file__)
    parser.usage.set_description(
        'This program co-registers two 3D volumes. The deformation is non-rigid and is '
        'constrained along Z direction (i.e., axial plane). Hence, this function assumes '
        'that orientation of the destination image is axial (RPI). If you need to register '
        'two volumes with large deformations and/or different contrasts, it is recommended to '
        'input spinal cord segmentations (binary mask) in order to achieve maximum robustness.'
        ' The program outputs a warping field that can be used to register other images to the'
        ' destination image. To apply the warping field to another image, use '
        'sct_apply_transfo')
    parser.add_option(name="-i",
                      type_value="file",
                      description="Image source.",
                      mandatory=True,
                      example="src.nii.gz")
    parser.add_option(name="-d",
                      type_value="file",
                      description="Image destination.",
                      mandatory=True,
                      example="dest.nii.gz")
    parser.add_option(name="-iseg",
                      type_value="file",
                      description="Segmentation source.",
                      mandatory=False,
                      example="src_seg.nii.gz")
    parser.add_option(name="-dseg",
                      type_value="file",
                      description="Segmentation destination.",
                      mandatory=False,
                      example="dest_seg.nii.gz")
    parser.add_option(
        name="-m",
        type_value="file",
        description=
        "Mask that can be created with sct_create_mask to improve accuracy over region of interest. "
        "This mask will be used on the destination image.",
        mandatory=False,
        example="mask.nii.gz")
    parser.add_option(name="-o",
                      type_value="file_output",
                      description="Name of output file.",
                      mandatory=False,
                      example="src_reg.nii.gz")
    parser.add_option(
        name="-p",
        type_value=[[':'], 'str'],
        description=
        """Parameters for registration. Separate arguments with ",". Separate steps with ":".\nstep: <int> Step number (starts at 1).\ntype: {im,seg} type of data used for registration.\nalgo: Default="""
        + paramreg.steps['1'].algo +
        """\n  global registration: {rigid,  affine,  syn,  bsplinesyn}\n  Slice By Slice registration: {slicereg: regularized translations (see: goo.gl/Sj3ZeU),  slicereg2d_translation: regularized using moving average (Hanning window),  slicereg2d_rigid,  slicereg2d_affine,  slicereg2d_pointwise: registration based on the Center of Mass of each slice (use only with type:Seg. Designed for centerlines), slicereg2d_bsplinesyn, slicereg2d_syn}\nmetric: {CC,MI,MeanSquares}. Default="""
        + paramreg.steps['1'].metric +
        """\niter: <int> Number of iterations. Default=""" +
        paramreg.steps['1'].iter +
        """\nshrink: <int> Shrink factor (only for SyN). Default=""" +
        paramreg.steps['1'].shrink +
        """\nsmooth: <int> Smooth factor (only for SyN). Default=""" +
        paramreg.steps['1'].smooth +
        """\ngradStep: <float> Gradient step. Default=""" +
        paramreg.steps['1'].gradStep +
        """\npoly: <int> Polynomial degree (only for slicereg). Default=""" +
        paramreg.steps['1'].poly +
        """\nwindow_length: <int> size of hanning window for smoothing along z for slicereg2d_pointwise, slicereg2d_translation, slicereg2d_rigid, slicereg2d_affine, slicereg2d_syn and slicereg2d_bsplinesyn.. Default="""
        + paramreg.steps['1'].window_length,
        mandatory=False,
        example=
        "step=1,type=seg,algo=slicereg,metric=MeanSquares:step=2,type=im,algo=syn,metric=MI,iter=5,shrink=2"
    )
    parser.add_option(
        name="-z",
        type_value="int",
        description=
        """size of z-padding to enable deformation at edges when using SyN.""",
        mandatory=False,
        default_value=param.padding)
    parser.add_option(name="-x",
                      type_value="multiple_choice",
                      description="""Final interpolation.""",
                      mandatory=False,
                      default_value='linear',
                      example=['nn', 'linear', 'spline'])
    parser.add_option(name="-r",
                      type_value="multiple_choice",
                      description="""Remove temporary files.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1'])
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="""Verbose.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1', '2'])
    arguments = parser.parse(sys.argv[1:])

    # get arguments
    fname_src = arguments['-i']
    fname_dest = arguments['-d']
    if '-iseg' in arguments:
        fname_src_seg = arguments['-iseg']
    if '-dseg' in arguments:
        fname_dest_seg = arguments['-dseg']
    if '-o' in arguments:
        fname_output = arguments['-o']
    if "-m" in arguments:
        fname_mask = arguments['-m']
    padding = arguments['-z']
    if "-p" in arguments:
        paramreg_user = arguments['-p']
        # update registration parameters
        for paramStep in paramreg_user:
            paramreg.addStep(paramStep)

    interp = arguments['-x']
    remove_temp_files = int(arguments['-r'])
    verbose = int(arguments['-v'])

    # Parameters for debug mode
    if param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
        status, path_sct_data = commands.getstatusoutput(
            'echo $SCT_TESTING_DATA_DIR')
        fname_dest = path_sct_data + '/mt/mt1.nii.gz'
        fname_src = path_sct_data + '/t2/t2.nii.gz'
        param_user = '******'
        remove_temp_files = '0'
        verbose = 1

    # print arguments
    print '\nInput parameters:'
    print '  Source .............. ' + fname_src
    print '  Destination ......... ' + fname_dest
    print '  Mask ................ ' + fname_mask
    print '  Output name ......... ' + fname_output
    # print '  Algorithm ........... '+paramreg.algo
    # print '  Number of iterations  '+paramreg.iter
    # print '  Metric .............. '+paramreg.metric
    print '  Remove temp files ... ' + str(remove_temp_files)
    print '  Verbose ............. ' + str(verbose)

    # update param
    param.verbose = verbose
    param.padding = padding
    param.fname_mask = fname_mask
    param.remove_temp_files = remove_temp_files

    # Get if input is 3D
    sct.printv('\nCheck if input data are 3D...', verbose)
    sct.check_if_3d(fname_src)
    sct.check_if_3d(fname_dest)

    # check if destination data is RPI
    sct.printv('\nCheck if destination data is RPI...', verbose)
    sct.check_if_rpi(fname_dest)

    # Extract path, file and extension
    path_src, file_src, ext_src = sct.extract_fname(fname_src)
    path_dest, file_dest, ext_dest = sct.extract_fname(fname_dest)

    # define output folder and file name
    if fname_output == '':
        path_out = ''  # output in user's current directory
        file_out = file_src + "_reg"
        ext_out = ext_src
    else:
        path_out, file_out, ext_out = sct.extract_fname(fname_output)

    # create temporary folder
    sct.printv('\nCreate temporary folder...', verbose)
    path_tmp = 'tmp.' + time.strftime("%y%m%d%H%M%S")
    status, output = sct.run('mkdir ' + path_tmp, verbose)

    # copy files to temporary folder
    sct.printv('\nCopy files...', verbose)
    sct.run('isct_c3d ' + fname_src + ' -o ' + path_tmp + '/src.nii', verbose)
    sct.run('isct_c3d ' + fname_dest + ' -o ' + path_tmp + '/dest.nii',
            verbose)
    if fname_src_seg:
        sct.run(
            'isct_c3d ' + fname_src_seg + ' -o ' + path_tmp + '/src_seg.nii',
            verbose)
        sct.run(
            'isct_c3d ' + fname_dest_seg + ' -o ' + path_tmp + '/dest_seg.nii',
            verbose)
    if not fname_mask == '':
        sct.run('isct_c3d ' + fname_mask + ' -o ' + path_tmp + '/mask.nii.gz',
                verbose)

    # go to tmp folder
    os.chdir(path_tmp)

    # Put source into destination space using header (no estimation -- purely based on header)
    # TODO: use c3d?
    # TODO: Check if necessary to do that
    # TODO: use that as step=0
    # sct.printv('\nPut source into destination space using header...', verbose)
    # sct.run('isct_antsRegistration -d 3 -t Translation[0] -m MI[dest_pad.nii,src.nii,1,16] -c 0 -f 1 -s 0 -o [regAffine,src_regAffine.nii] -n BSpline[3]', verbose)
    # if segmentation, also do it for seg

    # loop across registration steps
    warp_forward = []
    warp_inverse = []
    for i_step in range(0, len(paramreg.steps)):
        sct.printv(
            '\nEstimate transformation for step #' + str(i_step) + '...',
            param.verbose)
        # identify which is the src and dest
        if paramreg.steps[str(i_step)].type == 'im':
            src = 'src.nii'
            dest = 'dest.nii'
            interp_step = 'linear'
        elif paramreg.steps[str(i_step)].type == 'seg':
            src = 'src_seg.nii'
            dest = 'dest_seg.nii'
            interp_step = 'nn'
        else:
            sct.run('ERROR: Wrong image type.', 1, 'error')
        # if step>0, apply warp_forward_concat to the src image to be used
        if i_step > 0:
            sct.run(
                'sct_apply_transfo -i ' + src + ' -d ' + dest + ' -w ' +
                ','.join(warp_forward) + ' -o ' + sct.add_suffix(src, '_reg') +
                ' -x ' + interp_step, verbose)
            src = sct.add_suffix(src, '_reg')
        # register src --> dest
        warp_forward_out, warp_inverse_out = register(src, dest, paramreg,
                                                      param, str(i_step))
        warp_forward.append(warp_forward_out)
        warp_inverse.append(warp_inverse_out)

    # Put warp_forward_0 at the end of the list
    warp_forward_0 = warp_forward.pop(0)
    warp_forward.append(warp_forward_0)

    # Concatenate transformations
    sct.printv('\nConcatenate transformations...', verbose)
    sct.run(
        'sct_concat_transfo -w ' + ','.join(warp_forward) +
        ' -d dest.nii -o warp_src2dest.nii.gz', verbose)
    warp_inverse.reverse()
    sct.run(
        'sct_concat_transfo -w ' + ','.join(warp_inverse) +
        ' -d dest.nii -o warp_dest2src.nii.gz', verbose)

    # Apply warping field to src data
    sct.printv('\nApply transfo source --> dest...', verbose)
    sct.run(
        'sct_apply_transfo -i src.nii -o src_reg.nii -d dest.nii -w warp_src2dest.nii.gz -x '
        + interp, verbose)
    sct.printv('\nApply transfo dest --> source...', verbose)
    sct.run(
        'sct_apply_transfo -i dest.nii -o dest_reg.nii -d src.nii -w warp_dest2src.nii.gz -x '
        + interp, verbose)

    # come back to parent folder
    os.chdir('..')

    # Generate output files
    sct.printv('\nGenerate output files...', verbose)
    fname_src2dest = sct.generate_output_file(path_tmp + '/src_reg.nii',
                                              path_out + file_out + ext_out,
                                              verbose)
    sct.generate_output_file(
        path_tmp + '/warp_src2dest.nii.gz',
        path_out + 'warp_' + file_src + '2' + file_dest + '.nii.gz', verbose)
    fname_dest2src = sct.generate_output_file(
        path_tmp + '/dest_reg.nii', path_out + file_dest + '_reg' + ext_dest,
        verbose)
    sct.generate_output_file(
        path_tmp + '/warp_dest2src.nii.gz',
        path_out + 'warp_' + file_dest + '2' + file_src + '.nii.gz', verbose)
    # sct.generate_output_file(path_tmp+'/warp_dest2src.nii.gz', path_out+'warp_dest2src.nii.gz')

    # Delete temporary files
    if remove_temp_files:
        sct.printv('\nRemove temporary files...', verbose)
        sct.run('rm -rf ' + path_tmp, verbose)

    # display elapsed time
    elapsed_time = time.time() - start_time
    sct.printv(
        '\nFinished! Elapsed time: ' + str(int(round(elapsed_time))) + 's',
        verbose)
    sct.printv('\nTo view results, type:', verbose)
    sct.printv('fslview ' + fname_dest + ' ' + fname_src2dest + ' &', verbose,
               'info')
    sct.printv('fslview ' + fname_src + ' ' + fname_dest2src + ' &\n', verbose,
               'info')
Esempio n. 2
0
def main():
    
    #Initialization
    fname = ''
    verbose = param.verbose
    output_name = param.output_name
    smoothness = param.smoothness
         
    try:
         opts, args = getopt.getopt(sys.argv[1:],'hi:o:s:v:')
    except getopt.GetoptError:
        usage()
    for opt, arg in opts :
        if opt == '-h':
            usage()
        elif opt in ("-i"):
            fname = arg         
        elif opt in ("-o"):
            output_name = arg    
        elif opt in ("-s"):
            smoothness = arg    
        elif opt in ('-v'):
            verbose = int(arg)
    
    # display usage if a mandatory argument is not provided
    if fname == '' :
        usage()
    # check existence of input files
    print'\nCheck if file exists ...'
    
    sct.check_file_exist(fname)
    
    # check if RPI
    sct.check_if_rpi(fname)

    # Display arguments
    print'\nCheck input arguments...'
    print'  Input volume ...................... '+fname
    print'  Verbose ........................... '+str(verbose)

    file = load(fname)
    data = file.get_data()
    hdr = file.get_header()
    
    X,Y,Z = (data>0).nonzero()
    Z_new = linspace(min(Z),max(Z),(max(Z)-min(Z)+1))
    
    # tck1 = interpolate.splrep(Z, X, s=200)
  #   X_fit = interpolate.splev(Z_new, tck1)
  #
  #   tck2 = interpolate.splrep(Z, Y, s=200)
  #   Y_fit = interpolate.splev(Z_new, tck2)

    # f1 = interpolate.interp1d(Z, X, kind='cubic')
 #    f2 = interpolate.interp1d(Z,Y, kind='cubic')
 #

    # sort X and Y arrays using Z
    X = [X[i] for i in Z[:].argsort()]
    Y = [Y[i] for i in Z[:].argsort()]
    Z = [Z[i] for i in Z[:].argsort()]

    print X, Y, Z

    # NURBS!
    #X_fit, Y_fit, Z_fit, x_deriv, y_deriv, z_deriv = b_spline_nurbs(X, Y, Z, degree=3, point_number=3000)

    #f_opt_x, f_opt_y = opt_f(X,Y,Z)
    #print "f_opt = "+str(f_opt_x)+" "+str(f_opt_y)
    #f1 = non_parametric(Z,X,f=0.8)
    #f2 = non_parametric(Z,Y,f=0.8)

    f1 = interpolate.UnivariateSpline(Z, X)
    f2 = interpolate.UnivariateSpline(Z, Y)

    #f1 = polynomial_fit(Z,X,smoothness)
    #f2 = polynomial_fit(Z,Y,smoothness)
    
    X_fit = f1(Z_new)
    Y_fit = f2(Z_new)

    print X_fit
    print Y_fit

    if verbose==2 :
        import matplotlib.pyplot as plt

        plt.figure()
        plt.plot(Z_new,X_fit)
        plt.plot(Z,X,'o',linestyle = 'None')
        plt.show()

        plt.figure()
        plt.plot(Z_new,Y_fit)
        plt.plot(Z,Y,'o',linestyle = 'None')
        plt.show()
    
    data =data*0
    
    for i in xrange(len(X_fit)):
        data[X_fit[i],Y_fit[i],Z_new[i]] = 1
    
    
    print '\nSave volume ...'
    hdr.set_data_dtype('float32') # set imagetype to uint8
    # save volume
    #data = data.astype(float32, copy =False)
    img = Nifti1Image(data, None, hdr)
    file_name = output_name
    save(img,file_name)
    
    print '\nFile created : ' + output_name
    
    del data
def main():

    # Initialization
    fname_output = ''
    fname_mask = param.fname_mask
    fname_src_seg = ''
    fsloutput = 'export FSLOUTPUTTYPE=NIFTI; '  # for faster processing, all outputs are in NIFTI'

    start_time = time.time()
    # get path of the toolbox
    status, path_sct = commands.getstatusoutput('echo $SCT_DIR')

    # get default registration parameters
    # step1 = Paramreg(step='1', type='im', algo='syn', metric='MI', iter='5', shrink='1', smooth='0', gradStep='0.5')
    step0 = Paramreg(step='0', type='im', algo='syn', metric='MI', iter='0', shrink='1', smooth='0', gradStep='0.5')  # only used to put src into dest space
    step1 = Paramreg()
    paramreg = ParamregMultiStep([step0, step1])

    # Initialize the parser
    parser = Parser(__file__)
    parser.usage.set_description('This program co-registers two 3D volumes. The deformation is non-rigid and is '
                                 'constrained along Z direction (i.e., axial plane). Hence, this function assumes '
                                 'that orientation of the destination image is axial (RPI). If you need to register '
                                 'two volumes with large deformations and/or different contrasts, it is recommended to '
                                 'input spinal cord segmentations (binary mask) in order to achieve maximum robustness.'
                                 ' The program outputs a warping field that can be used to register other images to the'
                                 ' destination image. To apply the warping field to another image, use '
                                 'sct_apply_transfo')
    parser.add_option(name="-i",
                      type_value="file",
                      description="Image source.",
                      mandatory=True,
                      example="src.nii.gz")
    parser.add_option(name="-d",
                      type_value="file",
                      description="Image destination.",
                      mandatory=True,
                      example="dest.nii.gz")
    parser.add_option(name="-iseg",
                      type_value="file",
                      description="Segmentation source.",
                      mandatory=False,
                      example="src_seg.nii.gz")
    parser.add_option(name="-dseg",
                      type_value="file",
                      description="Segmentation destination.",
                      mandatory=False,
                      example="dest_seg.nii.gz")
    parser.add_option(name="-m",
                      type_value="file",
                      description="Binary mask to improve accuracy over region of interest.",
                      mandatory=False,
                      example="mask.nii.gz")
    parser.add_option(name="-o",
                      type_value="file_output",
                      description="Name of output file.",
                      mandatory=False,
                      example="src_reg.nii.gz")
    parser.add_option(name="-p",
                      type_value=[[':'],'str'],
                      description="""Parameters for registration. Separate arguments with ",". Separate steps with ":".\nstep: <int> Step number (starts at 1).\ntype: {im,seg} type of data used for registration.\nalgo: {slicereg,rigid,affine,syn,bsplinesyn}. Default="""+paramreg.steps['1'].algo+"""\n  For info about slicereg, see here: goo.gl/Sj3ZeU\nmetric: {CC,MI,MeanSquares}. Default="""+paramreg.steps['1'].metric+"""\niter: <int> Number of iterations. Default="""+paramreg.steps['1'].iter+"""\nshrink: <int> Shrink factor (only for SyN). Default="""+paramreg.steps['1'].shrink+"""\nsmooth: <int> Smooth factor (only for SyN). Default="""+paramreg.steps['1'].smooth+"""\ngradStep: <float> Gradient step (only for SyN). Default="""+paramreg.steps['1'].gradStep+"""\npoly: <int> Polynomial degree (only for slicereg). Default="""+paramreg.steps['1'].poly,
                      mandatory=False,
                      example="step=1,type=seg,algo=slicereg,metric=MeanSquares:step=2,type=im,algo=syn,metric=MI,iter=5,shrink=2")
    parser.add_option(name="-z",
                      type_value="int",
                      description="""size of z-padding to enable deformation at edges when using SyN.""",
                      mandatory=False,
                      default_value=param.padding)
    parser.add_option(name="-x",
                      type_value="multiple_choice",
                      description="""Final interpolation.""",
                      mandatory=False,
                      default_value='linear',
                      example=['nn', 'linear', 'spline'])
    parser.add_option(name="-r",
                      type_value="multiple_choice",
                      description="""Remove temporary files.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1'])
    parser.add_option(name="-v",
                      type_value="multiple_choice",
                      description="""Verbose.""",
                      mandatory=False,
                      default_value='1',
                      example=['0', '1', '2'])
    arguments = parser.parse(sys.argv[1:])

    # get arguments
    fname_src = arguments['-i']
    fname_dest = arguments['-d']
    if '-iseg' in arguments:
        fname_src_seg = arguments['-iseg']
    if '-dseg' in arguments:
        fname_dest_seg = arguments['-dseg']
    if '-o' in arguments:
        fname_output = arguments['-o']
    if "-m" in arguments:
        fname_mask = arguments['-m']
    padding = arguments['-z']
    if "-p" in arguments:
        paramreg_user = arguments['-p']
        # update registration parameters
        for paramStep in paramreg_user:
            paramreg.addStep(paramStep)

    interp = arguments['-x']
    remove_temp_files = int(arguments['-r'])
    verbose = int(arguments['-v'])

    # Parameters for debug mode
    if param.debug:
        print '\n*** WARNING: DEBUG MODE ON ***\n'
        status, path_sct_data = commands.getstatusoutput('echo $SCT_TESTING_DATA_DIR')
        fname_dest = path_sct_data+'/mt/mt1.nii.gz'
        fname_src = path_sct_data+'/t2/t2.nii.gz'
        param_user = '******'
        remove_temp_files = '0'
        verbose = 1

    # print arguments
    print '\nInput parameters:'
    print '  Source .............. '+fname_src
    print '  Destination ......... '+fname_dest
    print '  Mask ................ '+fname_mask
    print '  Output name ......... '+fname_output
    # print '  Algorithm ........... '+paramreg.algo
    # print '  Number of iterations  '+paramreg.iter
    # print '  Metric .............. '+paramreg.metric
    print '  Remove temp files ... '+str(remove_temp_files)
    print '  Verbose ............. '+str(verbose)

    # update param
    param.verbose = verbose
    param.padding = padding
    param.fname_mask = fname_mask

    # Get if input is 3D
    sct.printv('\nCheck if input data are 3D...', verbose)
    sct.check_if_3d(fname_src)
    sct.check_if_3d(fname_dest)

    # check if destination data is RPI
    sct.printv('\nCheck if destination data is RPI...', verbose)
    sct.check_if_rpi(fname_dest)

    # Extract path, file and extension
    path_src, file_src, ext_src = sct.extract_fname(fname_src)
    path_dest, file_dest, ext_dest = sct.extract_fname(fname_dest)

    # define output folder and file name
    if fname_output == '':
        path_out = ''  # output in user's current directory
        file_out = file_src+"_reg"
        ext_out = ext_src
    else:
        path_out, file_out, ext_out = sct.extract_fname(fname_output)

    # create temporary folder
    sct.printv('\nCreate temporary folder...', verbose)
    path_tmp = 'tmp.'+time.strftime("%y%m%d%H%M%S")
    status, output = sct.run('mkdir '+path_tmp, verbose)

    # copy files to temporary folder
    sct.printv('\nCopy files...', verbose)
    sct.run('isct_c3d '+fname_src+' -o '+path_tmp+'/src.nii', verbose)
    sct.run('isct_c3d '+fname_dest+' -o '+path_tmp+'/dest.nii', verbose)
    if fname_src_seg:
        sct.run('isct_c3d '+fname_src_seg+' -o '+path_tmp+'/src_seg.nii', verbose)
        sct.run('isct_c3d '+fname_dest_seg+' -o '+path_tmp+'/dest_seg.nii', verbose)
    if not fname_mask == '':
        sct.run('isct_c3d '+fname_mask+' -o '+path_tmp+'/mask.nii.gz', verbose)

    # go to tmp folder
    os.chdir(path_tmp)

    # Put source into destination space using header (no estimation -- purely based on header)
    # TODO: use c3d?
    # TODO: Check if necessary to do that
    # TODO: use that as step=0
    # sct.printv('\nPut source into destination space using header...', verbose)
    # sct.run('isct_antsRegistration -d 3 -t Translation[0] -m MI[dest_pad.nii,src.nii,1,16] -c 0 -f 1 -s 0 -o [regAffine,src_regAffine.nii] -n BSpline[3]', verbose)
    # if segmentation, also do it for seg

    # loop across registration steps
    warp_forward = []
    warp_inverse = []
    for i_step in range(0, len(paramreg.steps)):
        sct.printv('\nEstimate transformation for step #'+str(i_step)+'...', param.verbose)
        # identify which is the src and dest
        if paramreg.steps[str(i_step)].type == 'im':
            src = 'src.nii'
            dest = 'dest.nii'
            interp_step = 'linear'
        elif paramreg.steps[str(i_step)].type == 'seg':
            src = 'src_seg.nii'
            dest = 'dest_seg.nii'
            interp_step = 'nn'
        else:
            sct.run('ERROR: Wrong image type.', 1, 'error')
        # if step>0, apply warp_forward_concat to the src image to be used
        if i_step > 0:
            sct.run('sct_apply_transfo -i '+src+' -d '+dest+' -w '+','.join(warp_forward)+' -o '+sct.add_suffix(src, '_reg')+' -x '+interp_step, verbose)
            src = sct.add_suffix(src, '_reg')
        # register src --> dest
        warp_forward_out, warp_inverse_out = register(src, dest, paramreg, param, str(i_step))
        warp_forward.append(warp_forward_out)
        warp_inverse.append(warp_inverse_out)

    # Concatenate transformations
    sct.printv('\nConcatenate transformations...', verbose)
    sct.run('sct_concat_transfo -w '+','.join(warp_forward)+' -d dest.nii -o warp_src2dest.nii.gz', verbose)
    warp_inverse.reverse()
    sct.run('sct_concat_transfo -w '+','.join(warp_inverse)+' -d dest.nii -o warp_dest2src.nii.gz', verbose)

    # Apply warping field to src data
    sct.printv('\nApply transfo source --> dest...', verbose)
    sct.run('sct_apply_transfo -i src.nii -o src_reg.nii -d dest.nii -w warp_src2dest.nii.gz -x '+interp, verbose)
    sct.printv('\nApply transfo dest --> source...', verbose)
    sct.run('sct_apply_transfo -i dest.nii -o dest_reg.nii -d src.nii -w warp_dest2src.nii.gz -x '+interp, verbose)

    # come back to parent folder
    os.chdir('..')

    # Generate output files
    sct.printv('\nGenerate output files...', verbose)
    fname_src2dest = sct.generate_output_file(path_tmp+'/src_reg.nii', path_out+file_out+ext_out, verbose)
    sct.generate_output_file(path_tmp+'/warp_src2dest.nii.gz', path_out+'warp_'+file_src+'2'+file_dest+'.nii.gz', verbose)
    fname_dest2src = sct.generate_output_file(path_tmp+'/dest_reg.nii', path_out+file_dest+'_reg'+ext_dest, verbose)
    sct.generate_output_file(path_tmp+'/warp_dest2src.nii.gz', path_out+'warp_'+file_dest+'2'+file_src+'.nii.gz', verbose)
    # sct.generate_output_file(path_tmp+'/warp_dest2src.nii.gz', path_out+'warp_dest2src.nii.gz')

    # Delete temporary files
    if remove_temp_files:
        sct.printv('\nRemove temporary files...', verbose)
        sct.run('rm -rf '+path_tmp, verbose)

    # display elapsed time
    elapsed_time = time.time() - start_time
    sct.printv('\nFinished! Elapsed time: '+str(int(round(elapsed_time)))+'s', verbose)
    sct.printv('\nTo view results, type:', verbose)
    sct.printv('fslview '+fname_dest+' '+fname_src2dest+' &', verbose, 'info')
    sct.printv('fslview '+fname_src+' '+fname_dest2src+' &\n', verbose, 'info')