def freesurfer_create_subject_dir(basedir, T1dir, output_prefix):
from nipype.interfaces.io import FreeSurferSource
fs = FreeSurferSource()
fs.inputs.subjects_dir = experiment_dir
fs.inputs.subject_id = output_prefix
res = fs.run()
dir(res.outputs)
print res.outputs
def test_eulernumber(tmpdir):
# grab a surface from fsaverage
fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),
subject_id="fsaverage",
hemi="lh")
pial = fssrc.run().outputs.pial
assert isinstance(pial, str), "Problem when fetching surface file"
eu = fs.EulerNumber()
eu.inputs.in_file = pial
res = eu.run()
assert res.outputs.defects == 0
assert res.outputs.euler == 2
def test_mrisexpand(tmpdir):
fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),
subject_id='fsaverage', hemi='lh')
fsavginfo = fssrc.run().outputs.get()
# dt=60 to ensure very short runtime
expand_if = fs.MRIsExpand(in_file=fsavginfo['smoothwm'],
out_name='expandtmp',
distance=1,
dt=60)
expand_nd = pe.Node(
fs.MRIsExpand(in_file=fsavginfo['smoothwm'],
out_name='expandtmp',
distance=1,
dt=60),
name='expand_node')
# Interfaces should have same command line at instantiation
orig_cmdline = 'mris_expand -T 60 {} 1 expandtmp'.format(fsavginfo['smoothwm'])
assert expand_if.cmdline == orig_cmdline
assert expand_nd.interface.cmdline == orig_cmdline
# Run both interfaces
if_res = expand_if.run()
nd_res = expand_nd.run()
# Commandlines differ
node_cmdline = 'mris_expand -T 60 -pial {cwd}/lh.pial {cwd}/lh.smoothwm ' \
'1 expandtmp'.format(cwd=nd_res.runtime.cwd)
assert if_res.runtime.cmdline == orig_cmdline
assert nd_res.runtime.cmdline == node_cmdline
# Check output
if_out_file = if_res.outputs.get()['out_file']
nd_out_file = nd_res.outputs.get()['out_file']
# Same filename
assert op.basename(if_out_file) == op.basename(nd_out_file)
# Interface places output in source directory
assert op.dirname(if_out_file) == op.dirname(fsavginfo['smoothwm'])
# Node places output in working directory
assert op.dirname(nd_out_file) == nd_res.runtime.cwd
# Remove test surface
os.unlink(if_out_file)
def test_mrisexpand(tmpdir):
fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),
subject_id="fsaverage",
hemi="lh")
fsavginfo = fssrc.run().outputs.get()
# dt=60 to ensure very short runtime
expand_if = fs.MRIsExpand(in_file=fsavginfo["smoothwm"],
out_name="expandtmp",
distance=1,
dt=60)
expand_nd = pe.Node(
fs.MRIsExpand(in_file=fsavginfo["smoothwm"],
out_name="expandtmp",
distance=1,
dt=60),
name="expand_node",
)
# Interfaces should have same command line at instantiation
orig_cmdline = "mris_expand -T 60 {} 1 expandtmp".format(
fsavginfo["smoothwm"])
assert expand_if.cmdline == orig_cmdline
assert expand_nd.interface.cmdline == orig_cmdline
# Run Node interface
nd_res = expand_nd.run()
# Commandlines differ
node_cmdline = ("mris_expand -T 60 -pial {cwd}/lh.pial {cwd}/lh.smoothwm "
"1 expandtmp".format(cwd=nd_res.runtime.cwd))
assert nd_res.runtime.cmdline == node_cmdline
# Check output
if_out_file = expand_if._list_outputs()["out_file"]
nd_out_file = nd_res.outputs.get()["out_file"]
# Same filename
assert op.basename(if_out_file) == op.basename(nd_out_file)
# Interface places output in source directory
assert op.dirname(if_out_file) == op.dirname(fsavginfo["smoothwm"])
# Node places output in working directory
assert op.dirname(nd_out_file) == nd_res.runtime.cwd
