def test_robustregister():
filelist, outdir, cwd = create_files_in_directory()
reg = freesurfer.RobustRegister()
# make sure command gets called
yield assert_equal, reg.cmd, 'mri_robust_register'
# test raising error with mandatory args absent
yield assert_raises, ValueError, reg.run
# .inputs based parameters setting
reg.inputs.source_file = filelist[0]
reg.inputs.target_file = filelist[1]
reg.inputs.auto_sens = True
yield assert_equal, reg.cmdline, (
'mri_robust_register '
'--satit --lta %s_robustreg.lta --mov %s --dst %s' %
(filelist[0][:-4], filelist[0], filelist[1]))
# constructor based parameter setting
reg2 = freesurfer.RobustRegister(source_file=filelist[0],
target_file=filelist[1],
outlier_sens=3.0,
out_reg_file='foo.lta',
half_targ=True)
yield assert_equal, reg2.cmdline, (
'mri_robust_register --halfdst %s_halfway.nii --lta foo.lta '
'--sat 3.0000 --mov %s --dst %s' %
(os.path.join(outdir, filelist[1][:-4]), filelist[0], filelist[1]))
clean_directory(outdir, cwd)
def test_robustregister(create_files_in_directory):
filelist, outdir = create_files_in_directory
reg = freesurfer.RobustRegister()
cwd = os.getcwd()
# make sure command gets called
assert reg.cmd == "mri_robust_register"
# test raising error with mandatory args absent
with pytest.raises(ValueError):
reg.run()
# .inputs based parameters setting
reg.inputs.source_file = filelist[0]
reg.inputs.target_file = filelist[1]
reg.inputs.auto_sens = True
assert reg.cmdline == ("mri_robust_register --satit --lta "
"%s/%s_robustreg.lta --mov %s --dst %s" %
(cwd, filelist[0][:-4], filelist[0], filelist[1]))
# constructor based parameter setting
reg2 = freesurfer.RobustRegister(
source_file=filelist[0],
target_file=filelist[1],
outlier_sens=3.0,
out_reg_file="foo.lta",
half_targ=True,
)
assert reg2.cmdline == (
"mri_robust_register --halfdst %s_halfway.nii --lta foo.lta "
"--sat 3.0000 --mov %s --dst %s" %
(os.path.join(outdir, filelist[1][:-4]), filelist[0], filelist[1]))
def create_align_to_anatomy_workflow(name='align_to_anatomy',
format_string='inplane_to_anatomy'):
align_to_anatomy = pe.Workflow(name=name)
inputs = pe.Node(interface=util.IdentityInterface(
fields=['inplane_file', 'anatomy_file']),
name='inputs')
strip = pe.Node(interface=fs.ReconAll(),
name='strip') #FIXME: reconall interface barfs if rerun
strip.inputs.directive = 'autorecon1'
strip.inputs.flags = '-nowsgcaatlas'
register = pe.Node(interface=fs.RobustRegister(), name='register')
register.inputs.auto_sens = True
#register.inputs.init_orient = True #FIXME: disabled due to bug in binary
convert_xfm = pe.Node(interface=nmutil.LtaToXfm(), name='convert_xfm')
rename_xfm = pe.Node(interface=util.Rename(format_string),
name='rename_xfm')
rename_xfm.inputs.keep_ext = True
outputs = pe.Node(
interface=util.IdentityInterface(fields=['xfm_file', 'strip_file']),
name='outputs')
align_to_anatomy.connect(inputs, 'inplane_file', strip, 'T1_files')
align_to_anatomy.connect(strip, 'brainmask', register, 'source_file')
align_to_anatomy.connect(inputs, 'anatomy_file', register, 'target_file')
align_to_anatomy.connect(register, 'out_reg_file', convert_xfm, 'in_file')
align_to_anatomy.connect(convert_xfm, 'out_file', rename_xfm, 'in_file')
align_to_anatomy.connect(rename_xfm, 'out_file', outputs, 'xfm_file')
align_to_anatomy.connect(strip, 'brainmask', outputs, 'strip_file')
return align_to_anatomy
