def _run_interface(self, runtime):
from nipy.algorithms.registration import FmriRealign4d as FR4d
all_ims = [load_image(fname) for fname in self.inputs.in_file]
if not isdefined(self.inputs.tr_slices):
TR_slices = None
else:
TR_slices = self.inputs.tr_slices
R = FR4d(all_ims,
tr=self.inputs.tr,
slice_order=self.inputs.slice_order,
tr_slices=TR_slices,
time_interp=self.inputs.time_interp,
start=self.inputs.start)
R.estimate(loops=list(self.inputs.loops),
between_loops=list(self.inputs.between_loops),
speedup=list(self.inputs.speedup))
corr_run = R.resample()
self._out_file_path = []
self._par_file_path = []
for j, corr in enumerate(corr_run):
self._out_file_path.append(
os.path.abspath('corr_%s.nii.gz' %
(split_filename(self.inputs.in_file[j])[1])))
save_image(corr, self._out_file_path[j])
self._par_file_path.append(
os.path.abspath('%s.par' %
(os.path.split(self.inputs.in_file[j])[1])))
mfile = open(self._par_file_path[j], 'w')
motion = R._transforms[j]
# nipy does not encode euler angles. return in original form of
# translation followed by rotation vector see:
# http://en.wikipedia.org/wiki/Rodrigues'_rotation_formula
for i, mo in enumerate(motion):
params = [
'%.10f' % item
for item in np.hstack((mo.translation, mo.rotation))
]
string = ' '.join(params) + '\n'
mfile.write(string)
mfile.close()
return runtime
def _run_interface(self, runtime):
all_ims = [load_image(fname) for fname in self.inputs.in_file]
if not isdefined(self.inputs.tr_slices):
TR_slices = None
else:
TR_slices = self.inputs.tr_slices
R = FR4d(all_ims, tr=self.inputs.tr,
slice_order=self.inputs.slice_order,
tr_slices=TR_slices,
time_interp=self.inputs.time_interp,
start=self.inputs.start)
R.estimate(loops=self.inputs.loops,
between_loops=self.inputs.between_loops,
speedup=self.inputs.speedup)
corr_run = R.resample()
self._out_file_path = []
self._par_file_path = []
for j, corr in enumerate(corr_run):
self._out_file_path.append(os.path.abspath('corr_%s.nii.gz' %
(split_filename(self.inputs.in_file[j])[1])))
save_image(corr, self._out_file_path[j])
self._par_file_path.append(os.path.abspath('%s.par' %
(os.path.split(self.inputs.in_file[j])[1])))
mfile = open(self._par_file_path[j], 'w')
motion = R._transforms[j]
#output a .par file that looks like fsl.mcflirt's .par file
for i, mo in enumerate(motion):
params = ['%.10f' % item for item in np.hstack((mo.rotation,
mo.translation))]
string = ' '.join(params) + '\n'
mfile.write(string)
mfile.close()
return runtime