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')
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')