def main(self):
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
bse = tmpdir / "maskedbse.nrrd"
t2masked = tmpdir / "maskedt2.nrrd"
t2inbse = tmpdir / "t2inbse.nrrd"
epiwarp = tmpdir / "epiwarp.nii.gz"
t2tobse_rigid = tmpdir / "t2tobse_rigid"
logging.info('1. Extract and mask the DWI b0')
bse_py('-m', self.dwimask ,'-i', self.dwi ,'-o', bse)
logging.info("2. Mask the T2")
unu("3op", "ifelse", self.t2mask, self.t2, "0", "-o", t2masked)
logging.info(
"3. Compute a rigid registration from the T2 to the DWI baseline")
antsRegistrationSyN_sh("-d", "3"
,"-f", bse
,"-m", t2masked
,"-t", "r"
,"-o", tmpdir / "t2tobse_rigid")
antsApplyTransforms("-d", "3"
,"-i", t2masked
,"-o", t2inbse
,"-r", bse
,"-t", tmpdir / "t2tobse_rigid0GenericAffine.mat")
logging.info("4. Compute 1d nonlinear registration from the DWI to the T2 along the phase direction")
moving = bse
fixed = t2inbse
pre = tmpdir / "epi"
dwiepi = tmpdir / "dwiepi"+getext(self.out)
antsRegistration("-d", "3"
,"-m", "cc["+fixed+","+moving+",1,2]"
,"-t", "SyN[0.25,3,0]"
,"-c", "50x50x10"
,"-f", "4x2x1"
, "-s", "2x1x0"
,"--restrict-deformation", "0x1x0"
,"-v", "1"
,"-o", pre)
local.path(pre+"0Warp.nii.gz").move(epiwarp)
logging.info("5. Apply warp to the DWI")
antsApplyTransformsDWI_sh(self.dwi, self.dwimask, epiwarp, dwiepi)
if getext(dwiepi) == '.nhdr':
unu("save","-e","gzip","-f","nrrd","-i",dwiepi,self.out)
else:
dwiepi.move(self.out)
if self.debug:
tmpdir.move("epidebug-"+getpid())
def main(self):
fshome = local.path(os.getenv('FREESURFER_HOME'))
if not fshome:
logging.error('Set FREESURFER_HOME first.')
sys.exit(1)
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
b0masked = tmpdir / "b0masked.nrrd"
b0masked1mm = tmpdir / "b0masked1mm.nrrd"
brain = tmpdir / "brain.nii.gz"
wmparc = tmpdir / "wmparc.nii.gz"
brainmgz = self.parent.fsdir / 'mri/brain.mgz'
wmparcmgz = self.parent.fsdir / 'mri/wmparc.mgz'
wmparcindwi1mm = tmpdir / 'wmparcInDwi1mm.nii.gz'
logging.info(
"Make brain.nii.gz and wmparc.nii.gz from their mgz versions")
vol2vol = local[fshome / 'bin/mri_vol2vol']
label2vol = local[fshome / 'bin/mri_label2vol']
with local.env(SUBJECTS_DIR=''):
vol2vol('--mov', brainmgz, '--targ', brainmgz, '--regheader',
'--o', brain)
label2vol('--seg', wmparcmgz, '--temp', brainmgz,
'--regheader', wmparcmgz, '--o', wmparc)
logging.info('Extract B0 from DWI and mask')
bse_py('-i', self.parent.dwi, '-m', self.parent.dwimask, '-o',
b0masked)
logging.info('Made masked B0')
logging.info('Upsample masked baseline to 1x1x1')
ResampleImageBySpacing('3', b0masked, b0masked1mm, '1', '1', '1')
logging.info('Made 1x1x1 baseline')
logging.info('Register wmparc to B0')
pre = tmpdir / 'fsbrain_to_b0'
affine = pre + '0GenericAffine.mat'
warp = pre + '1Warp.nii.gz'
antsRegistrationSyNMI_sh['-m', brain, '-f', b0masked1mm, '-o', pre,
'-n', 32] & FG
antsApplyTransforms('-d', '3', '-i', wmparc, '-t', warp, affine,
'-r', b0masked1mm, '-o', wmparcindwi1mm,
'--interpolation', 'NearestNeighbor')
logging.info('Made ' + wmparcindwi1mm)
logging.info('Make output directory')
self.parent.out.mkdir()
b0masked.copy(self.parent.out)
b0masked1mm.copy(self.parent.out)
wmparcindwi1mm.copy(self.parent.out)
def main(self):
if not self.force and self.out.exists():
logging.error("'{}' already exists, use '--force' to force overwrite.".format(self.out))
sys.exit(1)
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
bse = tmpdir / "maskedbse.nrrd"
t2masked = tmpdir / "maskedt2.nrrd"
t2inbse = tmpdir / "t2inbse.nrrd"
epiwarp = tmpdir / "epiwarp.nii.gz"
t2tobse_rigid = tmpdir / "t2tobse_rigid"
logging.info('1. Extract and mask the DWI b0')
bse_py('-m', self.dwimask, '-i', self.dwi, '-o', bse)
logging.info("2. Mask the T2")
unu("3op", "ifelse", self.t2mask, self.t2, "0", "-o", t2masked)
logging.info(
"3. Compute a rigid registration from the T2 to the DWI baseline")
antsRegistrationSyN_sh("-d", "3", "-f", bse, "-m", t2masked, "-t",
"r", "-o", tmpdir / "t2tobse_rigid")
antsApplyTransforms("-d", "3", "-i", t2masked, "-o", t2inbse, "-r",
bse, "-t",
tmpdir / "t2tobse_rigid0GenericAffine.mat")
logging.info(
"4. Compute 1d nonlinear registration from the DWI to the T2 along the phase direction")
moving = bse
fixed = t2inbse
pre = tmpdir / "epi"
dwiepi = tmpdir / ("dwiepi" + ''.join(self.out.suffixes))
antsRegistration("-d", "3", "-m",
"cc[" + str(fixed) + "," + str(moving) + ",1,2]", "-t",
"SyN[0.25,3,0]", "-c", "50x50x10", "-f", "4x2x1",
"-s", "2x1x0", "--restrict-deformation", "0x1x0",
"-v", "1", "-o", pre)
local.path(str(pre) + "0Warp.nii.gz").move(epiwarp)
logging.info("5. Apply warp to the DWI")
antsApplyTransformsDWI_py('-i', self.dwi, '-m', self.dwimask, '-t', epiwarp, '-o', dwiepi)
if '.nhdr' in dwiepi.suffixes:
unu("save", "-e", "gzip", "-f", "nrrd", "-i", dwiepi, self.out)
else:
dwiepi.move(self.out)
if self.debug:
tmpdir.copy(self.out.dirname / ("epidebug-" + str(getpid())))
def main(self):
if not self.force and self.out.exists():
logging.error(
"'{}' already exists, use '--force' to force overwrite.".
format(self.out))
sys.exit(1)
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
bse = tmpdir / "maskedbse.nrrd"
t2masked = tmpdir / "maskedt2.nrrd"
t2inbse = tmpdir / "t2inbse.nrrd"
epiwarp = tmpdir / "epiwarp.nii.gz"
t2tobse_rigid = tmpdir / "t2tobse_rigid"
affine = tmpdir / "t2tobse_rigid0GenericAffine.mat"
logging.info('1. Extract and mask the DWI b0')
bse_py('-m', self.dwimask, '-i', self.dwi, '-o', bse)
logging.info("2. Mask the T2")
unu("3op", "ifelse", self.t2mask, self.t2, "0", "-o", t2masked)
logging.info(
"3. Compute a rigid registration from the T2 to the DWI baseline"
)
antsRegistrationSyN_sh("-d", "3", "-f", bse, "-m", t2masked, "-t",
"r", "-o", tmpdir / "t2tobse_rigid")
antsApplyTransforms("-d", "3", "-i", t2masked, "-o", t2inbse, "-r",
bse, "-t", affine)
logging.info(
"4. Compute 1d nonlinear registration from the DWI to the T2 along the phase direction"
)
moving = bse
fixed = t2inbse
pre = tmpdir / "epi"
dwiepi = tmpdir / ("dwiepi" + ''.join(self.out.suffixes))
antsRegistration("-d", "3", "-m",
"cc[" + str(fixed) + "," + str(moving) + ",1,2]",
"-t", "SyN[0.25,3,0]", "-c", "50x50x10", "-f",
"4x2x1", "-s", "2x1x0", "--restrict-deformation",
"0x1x0", "-v", "1", "-o", pre)
local.path(str(pre) + "0Warp.nii.gz").move(epiwarp)
logging.info("5. Apply warp to the DWI")
antsApplyTransformsDWI_py['-i', self.dwi, '-m', self.dwimask, '-t',
epiwarp, '-o', dwiepi, '-n',
str(self.nproc)] & FG
logging.info('6. Apply warp to the DWI mask')
epimask = self.out.dirname / self.out.basename.split(
'.')[0] + '-mask.nrrd'
antsApplyTransforms('-d', '3', '-i', self.dwimask, '-o', epimask,
'-n', 'NearestNeighbor', '-r', bse, '-t',
epiwarp)
unu('convert', '-t', 'uchar', '-i', epimask, '-o', epimask)
if '.nhdr' in dwiepi.suffixes:
unu("save", "-e", "gzip", "-f", "nrrd", "-i", dwiepi, "-o",
self.out)
else:
dwiepi.move(self.out)
# FIXME: the following conversion is only for UKFTractography, should be removed in future
if self.typeCast:
unu('convert', '-t', 'int16', '-i', self.out, '-o', self.out)
if self.debug:
tmpdir.copy(self.out.dirname / ("epidebug-" + str(getpid())))
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)
# fileinput() caused trouble reading data file in python 3, so switching to nrrd
# if the hdr has 'nan' in space origin, the following will take care of that
img = nrrd.read(self.dwi)
dwi = img[0]
hdr = img[1]
hdr_out = hdr.copy()
hdr_out['space origin'] = hdr_out['space origin'][0:3]
nrrd.write('dwijoined.nhdr',
dwi,
header=hdr_out,
compression_level=1)
# we want to use this hdr to write a new .nhdr file with corresponding data file
# so delete old data file from the hdr
if 'data file' in hdr_out.keys():
del hdr_out['data file']
elif 'datafile' in hdr_out.keys():
del hdr_out['datafile']
if 'content' in hdr_out.keys():
del hdr_out['content']
logging.info('Dice the DWI')
# Since fslmerge works along the 3rd axis only, dicing also has to be along that axis
# So, use `unu permute` to reorient the volumes to be stacked along 3rd axis only
# Include this issue in the tutorial
(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')
# use the following multi-processed loop
pool = Pool(int(self.nproc))
res = pool.map_async(_Register_vol, vols)
volsRegistered = res.get()
pool.close()
pool.join()
# or use the following for loop
# 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()
# nibabel loading can be avoided by setting 'data file' = EddyCorrect-DWI.nii.gz
# and 'byteskip' = -1
# Tashrif updated Pynrrd package to properly handle that
new_dwi = nib.load('EddyCorrect-DWI.nii.gz').get_data()
logging.info('Extract the rotations and realign the gradients')
space = hdr_out['space'].lower()
if (space == 'left'):
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]])
mf = np.matrix(hdr['measurement frame'])
# 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 (i, t) in enumerate(transforms):
gDir = [
float(num) for num in hdr_out['DWMRI_gradient_' +
'{:04}'.format(i)].split(' ')
if num
]
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
# compute 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)
hdr_out['DWMRI_gradient_' + '{:04}'.format(i)] = (' ').join(
str(x) for x in newdir.tolist()[0])
tar('cvzf', outxfms, transforms)
nrrd.write(self.out, new_dwi, header=hdr_out, compression_level=1)
if self.debug:
tmpdir.copy(
join(dirname(self.out), "eddy-debug-" + str(getpid())))
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()))