def compute(self):
in_image = self.getData('in')
zres = self.getVal('res[-3]')
yres = self.getVal('res[-2]')
xres = self.getVal('res[-1]')
inAffine = np.diag((zres, yres, xres, 1))
inWriter = partial(writeNifti, affine=inAffine)
# Nifti1 can't handle complex data, so we will use the magnitude if the
# inputs are complex
if in_image.dtype in complextypes:
in_image_ = IFilePath(inWriter, np.abs(in_image), suffix=".nii")
else:
in_image_ = IFilePath(inWriter, in_image, suffix=".nii")
brain_= OFilePath(readNifti)
seg_= OFilePath(readNifti)
bet = 'bet2'
Command(bet, in_image_, brain_)
fast = 'fast'
Command(fast, '-t {}'.format(self.getVal('contrast')+1),
'-o', seg_, brain_)
self.setData('brain', brain_.data(".nii.gz"))
self.setData('seg', seg_.data("_seg.nii.gz"))
[f.close() for f in (in_image_, brain_, seg_)]
return 0
def compute(self):
fixed = self.getData('fixed')
moving = self.getData('moving')
T = self.getData('init')
zres = self.getVal('res[-3]')
yres = self.getVal('res[-2]')
xres = self.getVal('res[-1]')
fixedAffine = movingAffine = np.diag((zres, yres, xres, 1))
fixedWriter = partial(writeNifti, affine=fixedAffine)
movingWriter = partial(writeNifti, affine=movingAffine)
# FLIRT can't handle complex data, so we will use the magnitude if the
# inputs are complex
if fixed.dtype in complextypes:
fixed_ = IFilePath(fixedWriter, np.abs(fixed), suffix=".nii")
else:
fixed_ = IFilePath(fixedWriter, fixed, suffix=".nii")
if moving.dtype in complextypes:
moving_ = IFilePath(movingWriter, np.abs(moving), suffix=".nii")
else:
moving_ = IFilePath(movingWriter, moving, suffix=".nii")
# this is where the registration is performed, unless an initial
# transformation matrix (T) is provided
out_ = None
if T is None:
out_ = OFilePath(readNifti, suffix=".nii.gz")
omat_ = OFilePath(np.loadtxt)
flirt = 'flirt'
if fixed.ndim == 2:
flirt += ' -2D'
Command(flirt,
'-dof {}'.format(self.getVal('dof')),
'-interp {}'.format(self.getVal('interp')),
'-cost {}'.format(self.getVal('cost')),
'-searchcost {}'.format(self.getVal('cost')),
'-coarsesearch {}.'.format(self.getVal('coarse search angle')),
'-finesearch {}'.format(self.getVal('fine search angle')),
'-searchrx -20 20', '-searchry -20 20', '-searchrz -20 20',
'-in', moving_, '-ref', fixed_, '-out', out_, '-omat', omat_)
T = omat_.data()
# magnitude images have been registered
# if the input is complex, apply the transformation to the real and
# imaginary channels separately (this requires running FLIRT two more
# times)
if moving.dtype in complextypes or out_ is None:
out = np.zeros(moving.shape, dtype=moving.dtype)
for ii in (np.real, np.imag):
if moving.dtype in realtypes and ii == np.imag:
continue
fixed_ = IFilePath(fixedWriter, ii(fixed), suffix=".nii")
moving_ = IFilePath(movingWriter, ii(moving), suffix=".nii")
T_ = IFilePath(np.savetxt, T)
out_ = OFilePath(readNifti, suffix=".nii.gz")
flirt = 'flirt -applyxfm'
if moving.ndim == 2:
flirt += ' -2D'
Command(flirt,
'-interp {}'.format(self.getVal('interp')),
'-init', T_, '-in', moving_, '-ref', fixed_, '-out', out_)
if ii == np.real:
out += out_.data()
else:
out += 1j * out_.data()
[f.close() for f in (fixed_, moving_, out_, T_)]
else:
# if the input is real, just use the output image from FLIRT
out = out_.data()
[f.close() for f in (fixed_, moving_, out_, omat_)]
self.setData('out', out)
self.setData('T', T)
return 0
def compute(self):
fixed = self.getData('fixed')
moving = self.getData('moving')
T = self.getData('init')
zres = self.getVal('res[-3]')
yres = self.getVal('res[-2]')
xres = self.getVal('res[-1]')
fixedAffine = movingAffine = np.diag((zres, yres, xres, 1))
fixedWriter = partial(writeNifti, affine=fixedAffine)
movingWriter = partial(writeNifti, affine=movingAffine)
# FLIRT can't handle complex data, so we will use the magnitude if the
# inputs are complex
if fixed.dtype in complextypes:
fixed_ = IFilePath(fixedWriter, np.abs(fixed), suffix=".nii")
else:
fixed_ = IFilePath(fixedWriter, fixed, suffix=".nii")
if moving.dtype in complextypes:
moving_ = IFilePath(movingWriter, np.abs(moving), suffix=".nii")
else:
moving_ = IFilePath(movingWriter, moving, suffix=".nii")
# this is where the registration is performed, unless an initial
# transformation matrix (T) is provided
out_ = None
if T is None:
out_ = OFilePath(readNifti, suffix=".nii.gz")
omat_ = OFilePath(np.loadtxt)
flirt = 'flirt'
if fixed.ndim == 2:
flirt += ' -2D'
Command(
flirt, '-dof {}'.format(self.getVal('dof')),
'-interp {}'.format(self.getVal('interp')),
'-cost {}'.format(self.getVal('cost')),
'-searchcost {}'.format(self.getVal('cost')),
'-coarsesearch {}.'.format(self.getVal('coarse search angle')),
'-finesearch {}'.format(self.getVal('fine search angle')),
'-searchrx -20 20', '-searchry -20 20', '-searchrz -20 20',
'-in', moving_, '-ref', fixed_, '-out', out_, '-omat', omat_)
T = omat_.data()
# magnitude images have been registered
# if the input is complex, apply the transformation to the real and
# imaginary channels separately (this requires running FLIRT two more
# times)
if moving.dtype in complextypes or out_ is None:
out = np.zeros(moving.shape, dtype=moving.dtype)
for ii in (np.real, np.imag):
if moving.dtype in realtypes and ii == np.imag:
continue
fixed_ = IFilePath(fixedWriter, ii(fixed), suffix=".nii")
moving_ = IFilePath(movingWriter, ii(moving), suffix=".nii")
T_ = IFilePath(np.savetxt, T)
out_ = OFilePath(readNifti, suffix=".nii.gz")
flirt = 'flirt -applyxfm'
if moving.ndim == 2:
flirt += ' -2D'
Command(flirt, '-interp {}'.format(self.getVal('interp')),
'-init', T_, '-in', moving_, '-ref', fixed_, '-out',
out_)
if ii == np.real:
out += out_.data()
else:
out += 1j * out_.data()
[f.close() for f in (fixed_, moving_, out_, T_)]
else:
# if the input is real, just use the output image from FLIRT
out = out_.data()
[f.close() for f in (fixed_, moving_, out_, omat_)]
self.setData('out', out)
self.setData('T', T)
return 0
