import commands, sys, os
from glob import glob
import nibabel
# Get path of the toolbox
status, path_sct = commands.getstatusoutput('echo $SCT_DIR')
# Append path that contains scripts, to be able to load modules
sys.path.append(path_sct + '/scripts')
sys.path.append(path_sct + '/dev/tamag')
from numpy import mean, append, isnan, array
import sct_utils as sct
from scipy import ndimage
from msct_register import register_slicereg2d_translation
path = '/Users/tamag/Desktop/test_register_multimodal/diff_size'
os.chdir(path)
src = 'T2_crop.nii.gz'
dest ='data_T2_RPI_crop.nii.gz'
# status, output = sct.run('sct_label_utils -i labels_vertebral.nii.gz -t display-voxel')
# nb = output.find('notation')
# int_nb = nb + 10
# labels = output[int_nb:]
register_slicereg2d_translation(dest, src, remove_temp_files=0, verbose=1)
def register(src, dest, paramreg, param, i_step_str):
# initiate default parameters of antsRegistration transformation
ants_registration_params = {'rigid': '', 'affine': '', 'compositeaffine': '', 'similarity': '', 'translation': '',
'bspline': ',10', 'gaussiandisplacementfield': ',3,0',
'bsplinedisplacementfield': ',5,10', 'syn': ',3,0', 'bsplinesyn': ',1,3'}
fsloutput = 'export FSLOUTPUTTYPE=NIFTI; ' # for faster processing, all outputs are in NIFTI'
# set metricSize
if paramreg.steps[i_step_str].metric == 'MI':
metricSize = '32' # corresponds to number of bins
else:
metricSize = '4' # corresponds to radius (for CC, MeanSquares...)
# set masking
if param.fname_mask:
fname_mask = 'mask.nii.gz'
masking = '-x mask.nii.gz'
else:
fname_mask = ''
masking = ''
if paramreg.steps[i_step_str].algo == 'slicereg':
from msct_image import find_zmin_zmax
# threshold images (otherwise, automatic crop does not work -- see issue #293)
src_th = sct.add_suffix(src, '_th')
sct.run(fsloutput+'fslmaths '+src+' -thr 0.1 '+src_th, param.verbose)
dest_th = sct.add_suffix(dest, '_th')
sct.run(fsloutput+'fslmaths '+dest+' -thr 0.1 '+dest_th, param.verbose)
# find zmin and zmax
zmin_src, zmax_src = find_zmin_zmax(src_th)
zmin_dest, zmax_dest = find_zmin_zmax(dest_th)
zmin_total = max([zmin_src, zmin_dest])
zmax_total = min([zmax_src, zmax_dest])
# crop data
src_crop = sct.add_suffix(src, '_crop')
sct.run('sct_crop_image -i '+src+' -o '+src_crop+' -dim 2 -start '+str(zmin_total)+' -end '+str(zmax_total), param.verbose)
dest_crop = sct.add_suffix(dest, '_crop')
sct.run('sct_crop_image -i '+dest+' -o '+dest_crop+' -dim 2 -start '+str(zmin_total)+' -end '+str(zmax_total), param.verbose)
# update variables
src = src_crop
dest = dest_crop
# estimate transfo
cmd = ('isct_antsSliceRegularizedRegistration '
'-t Translation[0.5] '
'-m '+paramreg.steps[i_step_str].metric+'['+dest+','+src+',1,'+metricSize+',Regular,0.2] '
'-p '+paramreg.steps[i_step_str].poly+' '
'-i '+paramreg.steps[i_step_str].iter+' '
'-f 1 '
'-s '+paramreg.steps[i_step_str].smooth+' '
'-v 1 ' # verbose (verbose=2 does not exist, so we force it to 1)
'-o [step'+i_step_str+','+src+'_regStep'+i_step_str+'.nii] ' # here the warp name is stage10 because antsSliceReg add "Warp"
+masking)
warp_forward_out = 'step'+i_step_str+'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str+'InverseWarp.nii.gz'
elif paramreg.steps[i_step_str].algo == 'slicereg2d_pointwise':
from msct_register import register_slicereg2d_pointwise
warp_forward_out = 'step'+i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_pointwise(src, dest, window_length=paramreg.steps[i_step_str].window_length, paramreg=Paramreg(step=paramreg.steps[i_step_str].step, type=paramreg.steps[i_step_str].type, algo='Translation', metric=paramreg.steps[i_step_str].metric, iter= paramreg.steps[i_step_str].iter, shrink=paramreg.steps[i_step_str].shrink, smooth=paramreg.steps[i_step_str].smooth, gradStep=paramreg.steps[i_step_str].gradStep),
warp_forward_out=warp_forward_out, warp_inverse_out=warp_inverse_out, factor=param.outlier_factor, verbose=param.verbose)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_translation':
from msct_register import register_slicereg2d_translation
warp_forward_out = 'step'+i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_translation(src, dest, window_length=paramreg.steps[i_step_str].window_length, paramreg=Paramreg(step=paramreg.steps[i_step_str].step, type=paramreg.steps[i_step_str].type, algo='Translation', metric=paramreg.steps[i_step_str].metric, iter= paramreg.steps[i_step_str].iter, shrink=paramreg.steps[i_step_str].shrink, smooth=paramreg.steps[i_step_str].smooth, gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask, warp_forward_out=warp_forward_out, warp_inverse_out=warp_inverse_out, factor=param.outlier_factor, remove_temp_files=param.remove_temp_files,
verbose=param.verbose, ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_rigid':
from msct_register import register_slicereg2d_rigid
warp_forward_out = 'step'+i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_rigid(src, dest, window_length=paramreg.steps[i_step_str].window_length, paramreg=Paramreg(step=paramreg.steps[i_step_str].step, type=paramreg.steps[i_step_str].type, algo='Rigid', metric=paramreg.steps[i_step_str].metric, iter= paramreg.steps[i_step_str].iter, shrink=paramreg.steps[i_step_str].shrink, smooth=paramreg.steps[i_step_str].smooth, gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask, warp_forward_out=warp_forward_out, warp_inverse_out=warp_inverse_out, factor=param.outlier_factor, remove_temp_files=param.remove_temp_files,
verbose=param.verbose, ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_affine':
from msct_register import register_slicereg2d_affine
warp_forward_out = 'step'+i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_affine(src, dest, window_length=paramreg.steps[i_step_str].window_length, paramreg=Paramreg(step=paramreg.steps[i_step_str].step, type=paramreg.steps[i_step_str].type, algo='Affine', metric=paramreg.steps[i_step_str].metric, iter= paramreg.steps[i_step_str].iter, shrink=paramreg.steps[i_step_str].shrink, smooth=paramreg.steps[i_step_str].smooth, gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask, warp_forward_out=warp_forward_out, warp_inverse_out=warp_inverse_out, factor=param.outlier_factor, remove_temp_files=param.remove_temp_files,
verbose=param.verbose, ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_syn':
from msct_register import register_slicereg2d_syn
warp_forward_out = 'step'+i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_syn(src, dest, window_length=paramreg.steps[i_step_str].window_length, paramreg=Paramreg(step=paramreg.steps[i_step_str].step, type=paramreg.steps[i_step_str].type, algo='SyN', metric=paramreg.steps[i_step_str].metric, iter= paramreg.steps[i_step_str].iter, shrink=paramreg.steps[i_step_str].shrink, smooth=paramreg.steps[i_step_str].smooth, gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask, warp_forward_out=warp_forward_out, warp_inverse_out=warp_inverse_out, factor=param.outlier_factor, remove_temp_files=param.remove_temp_files,
verbose=param.verbose, ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_bsplinesyn':
from msct_register import register_slicereg2d_bsplinesyn
warp_forward_out = 'step'+i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_bsplinesyn(src, dest, window_length=paramreg.steps[i_step_str].window_length, paramreg=Paramreg(step=paramreg.steps[i_step_str].step, type=paramreg.steps[i_step_str].type, algo='BSplineSyN', metric=paramreg.steps[i_step_str].metric, iter= paramreg.steps[i_step_str].iter, shrink=paramreg.steps[i_step_str].shrink, smooth=paramreg.steps[i_step_str].smooth, gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask, warp_forward_out=warp_forward_out, warp_inverse_out=warp_inverse_out, factor=param.outlier_factor, remove_temp_files=param.remove_temp_files,
verbose=param.verbose, ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo.lower() in ants_registration_params:
from msct_image import pad_image
# Pad the destination image (because ants doesn't deform the extremities)
# N.B. no need to pad if iter = 0
if not paramreg.steps[i_step_str].iter == '0':
dest_pad = sct.add_suffix(dest, '_pad')
pad_image(dest, dest_pad, param.padding)
dest = dest_pad
cmd = ('isct_antsRegistration '
'--dimensionality 3 '
'--transform '+paramreg.steps[i_step_str].algo+'['+paramreg.steps[i_step_str].gradStep +
ants_registration_params[paramreg.steps[i_step_str].algo.lower()]+'] '
'--metric '+paramreg.steps[i_step_str].metric+'['+dest+','+src+',1,'+metricSize+'] '
'--convergence '+paramreg.steps[i_step_str].iter+' '
'--shrink-factors '+paramreg.steps[i_step_str].shrink+' '
'--smoothing-sigmas '+paramreg.steps[i_step_str].smooth+'mm '
'--restrict-deformation 1x1x0 '
'--output [step'+i_step_str+','+src+'_regStep'+i_step_str+'.nii] '
'--interpolation BSpline[3] '
+masking)
if param.verbose >= 1:
cmd += ' --verbose 1'
if paramreg.steps[i_step_str].algo in ['rigid', 'affine']:
warp_forward_out = 'step'+i_step_str+'0GenericAffine.mat'
warp_inverse_out = '-step'+i_step_str+'0GenericAffine.mat'
else:
warp_forward_out = 'step'+i_step_str+'0Warp.nii.gz'
warp_inverse_out = 'step'+i_step_str+'0InverseWarp.nii.gz'
else:
sct.printv('\nERROR: algo '+paramreg.steps[i_step_str].algo+' does not exist. Exit program\n', 1, 'error')
# run registration
status, output = sct.run(cmd, param.verbose)
if os.path.isfile(warp_forward_out):
# rename warping fields
if paramreg.steps[i_step_str].algo in ['rigid', 'affine']:
warp_forward = 'warp_forward_'+i_step_str+'.mat'
os.rename(warp_forward_out, warp_forward)
warp_inverse = '-warp_forward_'+i_step_str+'.mat'
else:
warp_forward = 'warp_forward_'+i_step_str+'.nii.gz'
warp_inverse = 'warp_inverse_'+i_step_str+'.nii.gz'
os.rename(warp_forward_out, warp_forward)
os.rename(warp_inverse_out, warp_inverse)
else:
sct.printv(output, 1, 'error')
sct.printv('\nERROR: ANTs failed. Exit program.\n', 1, 'error')
return warp_forward, warp_inverse
def register(src, dest, paramreg, param, i_step_str):
# initiate default parameters of antsRegistration transformation
ants_registration_params = {
'rigid': '',
'affine': '',
'compositeaffine': '',
'similarity': '',
'translation': '',
'bspline': ',10',
'gaussiandisplacementfield': ',3,0',
'bsplinedisplacementfield': ',5,10',
'syn': ',3,0',
'bsplinesyn': ',1,3'
}
fsloutput = 'export FSLOUTPUTTYPE=NIFTI; ' # for faster processing, all outputs are in NIFTI'
# set metricSize
if paramreg.steps[i_step_str].metric == 'MI':
metricSize = '32' # corresponds to number of bins
else:
metricSize = '4' # corresponds to radius (for CC, MeanSquares...)
# set masking
if param.fname_mask:
fname_mask = 'mask.nii.gz'
masking = '-x mask.nii.gz'
else:
fname_mask = ''
masking = ''
if paramreg.steps[i_step_str].algo == 'slicereg':
from msct_image import find_zmin_zmax
# threshold images (otherwise, automatic crop does not work -- see issue #293)
src_th = sct.add_suffix(src, '_th')
from msct_image import Image
nii = Image(src)
data = nii.data
data[data < 0.1] = 0
nii.data = data
nii.setFileName(src_th)
nii.save()
# sct.run(fsloutput+'fslmaths '+src+' -thr 0.1 '+src_th, param.verbose)
dest_th = sct.add_suffix(dest, '_th')
nii = Image(dest)
data = nii.data
data[data < 0.1] = 0
nii.data = data
nii.setFileName(dest_th)
nii.save()
# sct.run(fsloutput+'fslmaths '+dest+' -thr 0.1 '+dest_th, param.verbose)
# find zmin and zmax
zmin_src, zmax_src = find_zmin_zmax(src_th)
zmin_dest, zmax_dest = find_zmin_zmax(dest_th)
zmin_total = max([zmin_src, zmin_dest])
zmax_total = min([zmax_src, zmax_dest])
# crop data
src_crop = sct.add_suffix(src, '_crop')
sct.run(
'sct_crop_image -i ' + src + ' -o ' + src_crop +
' -dim 2 -start ' + str(zmin_total) + ' -end ' + str(zmax_total),
param.verbose)
dest_crop = sct.add_suffix(dest, '_crop')
sct.run(
'sct_crop_image -i ' + dest + ' -o ' + dest_crop +
' -dim 2 -start ' + str(zmin_total) + ' -end ' + str(zmax_total),
param.verbose)
# update variables
src = src_crop
dest = dest_crop
# estimate transfo
cmd = (
'isct_antsSliceRegularizedRegistration '
'-t Translation[0.5] '
'-m ' + paramreg.steps[i_step_str].metric + '[' + dest + ',' +
src + ',1,' + metricSize + ',Regular,0.2] '
'-p ' + paramreg.steps[i_step_str].poly + ' '
'-i ' + paramreg.steps[i_step_str].iter + ' '
'-f 1 '
'-s ' + paramreg.steps[i_step_str].smooth + ' '
'-v 1 ' # verbose (verbose=2 does not exist, so we force it to 1)
'-o [step' + i_step_str + ',' + src + '_regStep' + i_step_str +
'.nii] ' # here the warp name is stage10 because antsSliceReg add "Warp"
+ masking)
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
elif paramreg.steps[i_step_str].algo == 'slicereg2d_pointwise':
from msct_register import register_slicereg2d_pointwise
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_pointwise(
src,
dest,
window_length=paramreg.steps[i_step_str].window_length,
paramreg=Paramreg(step=paramreg.steps[i_step_str].step,
type=paramreg.steps[i_step_str].type,
algo='Translation',
metric=paramreg.steps[i_step_str].metric,
iter=paramreg.steps[i_step_str].iter,
shrink=paramreg.steps[i_step_str].shrink,
smooth=paramreg.steps[i_step_str].smooth,
gradStep=paramreg.steps[i_step_str].gradStep),
warp_forward_out=warp_forward_out,
warp_inverse_out=warp_inverse_out,
factor=param.outlier_factor,
verbose=param.verbose)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_translation':
from msct_register import register_slicereg2d_translation
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_translation(
src,
dest,
window_length=paramreg.steps[i_step_str].window_length,
paramreg=Paramreg(step=paramreg.steps[i_step_str].step,
type=paramreg.steps[i_step_str].type,
algo='Translation',
metric=paramreg.steps[i_step_str].metric,
iter=paramreg.steps[i_step_str].iter,
shrink=paramreg.steps[i_step_str].shrink,
smooth=paramreg.steps[i_step_str].smooth,
gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask,
warp_forward_out=warp_forward_out,
warp_inverse_out=warp_inverse_out,
factor=param.outlier_factor,
remove_temp_files=param.remove_temp_files,
verbose=param.verbose,
ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_rigid':
from msct_register import register_slicereg2d_rigid
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_rigid(
src,
dest,
window_length=paramreg.steps[i_step_str].window_length,
paramreg=Paramreg(step=paramreg.steps[i_step_str].step,
type=paramreg.steps[i_step_str].type,
algo='Rigid',
metric=paramreg.steps[i_step_str].metric,
iter=paramreg.steps[i_step_str].iter,
shrink=paramreg.steps[i_step_str].shrink,
smooth=paramreg.steps[i_step_str].smooth,
gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask,
warp_forward_out=warp_forward_out,
warp_inverse_out=warp_inverse_out,
factor=param.outlier_factor,
remove_temp_files=param.remove_temp_files,
verbose=param.verbose,
ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_affine':
from msct_register import register_slicereg2d_affine
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_affine(
src,
dest,
window_length=paramreg.steps[i_step_str].window_length,
paramreg=Paramreg(step=paramreg.steps[i_step_str].step,
type=paramreg.steps[i_step_str].type,
algo='Affine',
metric=paramreg.steps[i_step_str].metric,
iter=paramreg.steps[i_step_str].iter,
shrink=paramreg.steps[i_step_str].shrink,
smooth=paramreg.steps[i_step_str].smooth,
gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask,
warp_forward_out=warp_forward_out,
warp_inverse_out=warp_inverse_out,
factor=param.outlier_factor,
remove_temp_files=param.remove_temp_files,
verbose=param.verbose,
ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_syn':
from msct_register import register_slicereg2d_syn
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_syn(
src,
dest,
window_length=paramreg.steps[i_step_str].window_length,
paramreg=Paramreg(step=paramreg.steps[i_step_str].step,
type=paramreg.steps[i_step_str].type,
algo='SyN',
metric=paramreg.steps[i_step_str].metric,
iter=paramreg.steps[i_step_str].iter,
shrink=paramreg.steps[i_step_str].shrink,
smooth=paramreg.steps[i_step_str].smooth,
gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask,
warp_forward_out=warp_forward_out,
warp_inverse_out=warp_inverse_out,
factor=param.outlier_factor,
remove_temp_files=param.remove_temp_files,
verbose=param.verbose,
ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo == 'slicereg2d_bsplinesyn':
from msct_register import register_slicereg2d_bsplinesyn
warp_forward_out = 'step' + i_step_str + 'Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + 'InverseWarp.nii.gz'
register_slicereg2d_bsplinesyn(
src,
dest,
window_length=paramreg.steps[i_step_str].window_length,
paramreg=Paramreg(step=paramreg.steps[i_step_str].step,
type=paramreg.steps[i_step_str].type,
algo='BSplineSyN',
metric=paramreg.steps[i_step_str].metric,
iter=paramreg.steps[i_step_str].iter,
shrink=paramreg.steps[i_step_str].shrink,
smooth=paramreg.steps[i_step_str].smooth,
gradStep=paramreg.steps[i_step_str].gradStep),
fname_mask=fname_mask,
warp_forward_out=warp_forward_out,
warp_inverse_out=warp_inverse_out,
factor=param.outlier_factor,
remove_temp_files=param.remove_temp_files,
verbose=param.verbose,
ants_registration_params=ants_registration_params)
cmd = ('')
elif paramreg.steps[i_step_str].algo.lower() in ants_registration_params:
from msct_image import pad_image
# Pad the destination image (because ants doesn't deform the extremities)
# N.B. no need to pad if iter = 0
if not paramreg.steps[i_step_str].iter == '0':
dest_pad = sct.add_suffix(dest, '_pad')
pad_image(dest, dest_pad, param.padding)
dest = dest_pad
cmd = (
'isct_antsRegistration '
'--dimensionality 3 '
'--transform ' + paramreg.steps[i_step_str].algo + '[' +
paramreg.steps[i_step_str].gradStep +
ants_registration_params[paramreg.steps[i_step_str].algo.lower()] +
'] '
'--metric ' + paramreg.steps[i_step_str].metric + '[' + dest +
',' + src + ',1,' + metricSize + '] '
'--convergence ' + paramreg.steps[i_step_str].iter + ' '
'--shrink-factors ' + paramreg.steps[i_step_str].shrink + ' '
'--smoothing-sigmas ' + paramreg.steps[i_step_str].smooth + 'mm '
'--restrict-deformation 1x1x0 '
'--output [step' + i_step_str + ',' + src + '_regStep' +
i_step_str + '.nii] '
'--interpolation BSpline[3] ' + masking)
if param.verbose >= 1:
cmd += ' --verbose 1'
if paramreg.steps[i_step_str].algo in ['rigid', 'affine']:
warp_forward_out = 'step' + i_step_str + '0GenericAffine.mat'
warp_inverse_out = '-step' + i_step_str + '0GenericAffine.mat'
else:
warp_forward_out = 'step' + i_step_str + '0Warp.nii.gz'
warp_inverse_out = 'step' + i_step_str + '0InverseWarp.nii.gz'
else:
sct.printv(
'\nERROR: algo ' + paramreg.steps[i_step_str].algo +
' does not exist. Exit program\n', 1, 'error')
# run registration
status, output = sct.run(cmd, param.verbose)
if os.path.isfile(warp_forward_out):
# rename warping fields
if paramreg.steps[i_step_str].algo in ['rigid', 'affine']:
warp_forward = 'warp_forward_' + i_step_str + '.mat'
os.rename(warp_forward_out, warp_forward)
warp_inverse = '-warp_forward_' + i_step_str + '.mat'
else:
warp_forward = 'warp_forward_' + i_step_str + '.nii.gz'
warp_inverse = 'warp_inverse_' + i_step_str + '.nii.gz'
os.rename(warp_forward_out, warp_forward)
os.rename(warp_inverse_out, warp_inverse)
else:
sct.printv(output, 1, 'error')
sct.printv('\nERROR: ANTs failed. Exit program.\n', 1, 'error')
return warp_forward, warp_inverse
#!/usr/bin/env python
import commands, sys, os
from glob import glob
import nibabel
# Get path of the toolbox
status, path_sct = commands.getstatusoutput('echo $SCT_DIR')
# Append path that contains scripts, to be able to load modules
sys.path.append(path_sct + '/scripts')
sys.path.append(path_sct + '/dev/tamag')
from numpy import mean, append, isnan, array
import sct_utils as sct
from scipy import ndimage
from msct_register import register_slicereg2d_translation
path = '/Users/tamag/Desktop/test_register_multimodal/diff_size'
os.chdir(path)
src = 'T2_crop.nii.gz'
dest = 'data_T2_RPI_crop.nii.gz'
# status, output = sct.run('sct_label_utils -i labels_vertebral.nii.gz -t display-voxel')
# nb = output.find('notation')
# int_nb = nb + 10
# labels = output[int_nb:]
register_slicereg2d_translation(dest, src, remove_temp_files=0, verbose=1)
