def test_synthesizeflash(create_files_in_directory):
filelist, outdir = create_files_in_directory
syn = freesurfer.SynthesizeFLASH()
# make sure command gets called
assert syn.cmd == "mri_synthesize"
# test raising error with mandatory args absent
with pytest.raises(ValueError):
syn.run()
# .inputs based parameters setting
syn.inputs.t1_image = filelist[0]
syn.inputs.pd_image = filelist[1]
syn.inputs.flip_angle = 30
syn.inputs.te = 4.5
syn.inputs.tr = 20
assert syn.cmdline == (
"mri_synthesize 20.00 30.00 4.500 %s %s %s" %
(filelist[0], filelist[1], os.path.join(outdir, "synth-flash_30.mgz")))
# constructor based parameters setting
syn2 = freesurfer.SynthesizeFLASH(t1_image=filelist[0],
pd_image=filelist[1],
flip_angle=20,
te=5,
tr=25)
assert syn2.cmdline == (
"mri_synthesize 25.00 20.00 5.000 %s %s %s" %
(filelist[0], filelist[1], os.path.join(outdir, "synth-flash_20.mgz")))
def test_synthesizeflash():
filelist, outdir, cwd = create_files_in_directory()
syn = freesurfer.SynthesizeFLASH()
# make sure command gets called
yield assert_equal, syn.cmd, 'mri_synthesize'
# test raising error with mandatory args absent
yield assert_raises, ValueError, syn.run
# .inputs based parameters setting
syn.inputs.t1_image = filelist[0]
syn.inputs.pd_image = filelist[1]
syn.inputs.flip_angle = 30
syn.inputs.te = 4.5
syn.inputs.tr = 20
yield assert_equal, syn.cmdline, (
'mri_synthesize 20.00 30.00 4.500 %s %s %s' %
(filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_30.mgz')))
# constructor based parameters setting
syn2 = freesurfer.SynthesizeFLASH(t1_image=filelist[0],
pd_image=filelist[1],
flip_angle=20,
te=5,
tr=25)
yield assert_equal, syn2.cmdline, (
'mri_synthesize 25.00 20.00 5.000 %s %s %s' %
(filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_20.mgz')))