def _Register_vol(volnii):
logging.info('Run FSL flirt affine registration')
flirt('-interp', 'sinc', '-sincwidth', '7', '-sincwindow', 'blackman',
'-in', volnii, '-ref', 'b0.nii.gz', '-nosearch', '-o', volnii,
'-omat', volnii.with_suffix('.txt', depth=2), '-paddingsize', '1')
return volnii
def _Register_vol(vol):
volnii = vol.with_suffix('.nii.gz')
ConvertBetweenFileFormats(vol, volnii, 'short')
logging.info('Run FSL flirt affine registration')
flirt('-interp', 'sinc', '-sincwidth', '7', '-sincwindow', 'blackman',
'-in', volnii, '-ref', 'b0.nii.gz', '-nosearch', '-o', volnii,
'-omat', volnii.with_suffix('.txt', depth=2), '-paddingsize', '1')
return volnii
def main(self):
self.out = local.path(self.out)
if self.out.exists():
if self.overwrite:
self.out.delete()
else:
logging.error(
"{} exists, use '--force' to overwrite it".format(
self.out))
sys.exit(1)
outxfms = self.out.dirname / self.out.stem + '-xfms.tgz'
with TemporaryDirectory() as tmpdir, local.cwd(tmpdir):
tmpdir = local.path(tmpdir)
unu('save', '-f', 'nrrd', '-e', 'gzip', '-i', self.dwi, '-o',
'dwijoined.nhdr')
logging.info('Dice the DWI')
(unu['convert', '-t', 'int16', '-i', 'dwijoined.nhdr']
| unu['dice', '-a', '3', '-o', 'Diffusion-G'])()
vols = tmpdir.glob('Diffusion-G*.nrrd')
vols.sort()
logging.info('Extract the B0')
bse_py('-i', 'dwijoined.nhdr', '-o', 'b0.nrrd')
ConvertBetweenFileFormats('b0.nrrd', 'b0.nii.gz', 'short')
logging.info('Register each volume to the B0')
volsRegistered = []
for vol in vols:
volnii = vol.with_suffix('.nii.gz')
ConvertBetweenFileFormats(vol, volnii, 'short')
logging.info('Run FSL flirt affine registration')
flirt('-interp', 'sinc', '-sincwidth', '7', '-sincwindow',
'blackman', '-in', volnii, '-ref', 'b0.nii.gz',
'-nosearch', '-o', volnii, '-omat',
volnii.with_suffix('.txt', depth=2), '-paddingsize', '1')
volsRegistered.append(volnii)
fslmerge('-t', 'EddyCorrect-DWI', volsRegistered)
transforms = tmpdir.glob('Diffusion-G*.txt')
transforms.sort()
logging.info('Extract the rotations and realign the gradients')
gDir = []
header = ''
gNum = []
gframe = []
with open('dwijoined.nhdr') as f:
for line in f:
if line.find('DWMRI_gradient_') != -1:
gNum.append(line[15:19])
gDir.append(map(float, line[21:-1].split()))
elif line.find('data file:') != -1:
header = header + 'data file: EddyCorrect-DWI.nii.gz\n'
elif line.find('encoding:') != -1:
header = header + line + 'byteskip: -1\n'
elif line.find('measurement frame:') != -1:
header = header + line
mf = np.matrix([
map(float,
line.split()[2][1:-1].split(',')),
map(float,
line.split()[3][1:-1].split(',')),
map(float,
line.split()[4][1:-1].split(','))
])
elif line.find('space:') != -1:
header = header + line
# Here I assume either lps or ras so only need to check the first letter
space = line.split()[1][0]
if (space == 'l') | (space == 'L'):
spctoras = np.matrix([[-1, 0, 0], [0, -1, 0],
[0, 0, 1]])
else:
spctoras = np.matrix([[1, 0, 0], [0, 1, 0],
[0, 0, 1]])
else:
header = header + line
with open('EddyCorrect-DWI.nhdr', 'w') as f:
f.write(header)
i = 0
# Transforms are in RAS so need to do inv(MF)*inv(SPC2RAS)*ROTATION*SPC2RAS*MF*GRADIENT
mfras = mf.I * spctoras.I
rasmf = spctoras * mf
for t in transforms:
logging.info('Apply ' + t)
tra = np.loadtxt(t)
#removes the translation
aff = np.matrix(tra[0:3, 0:3])
# computes the finite strain of aff to get the rotation
rot = aff * aff.T
# Computer the square root of rot
[el, ev] = np.linalg.eig(rot)
eL = np.identity(3) * np.sqrt(el)
sq = ev * eL * ev.I
# finally the rotation is defined as
rot = sq.I * aff
newdir = np.dot(mfras * rot * rasmf, gDir[i])
f.write('DWMRI_gradient_' + gNum[i] + ':= ' +
str(newdir[0, 0]) + ' ' + str(newdir[0, 1]) + ' ' +
str(newdir[0, 2]) + '\n')
i = i + 1
tar('cvzf', outxfms, transforms)
unu('save', '-f', 'nrrd', '-e', 'gzip', '-i',
'EddyCorrect-DWI.nhdr', '-o', self.out)
if self.debug:
tmpdir.move("eddy-debug-" + str(getpid()))