def main(self):
with TemporaryDirectory() as t:
t = local.path(t)
ukf = self.ukf
fsindwi = self.fsindwi
if nrrd(self.fsindwi):
fsindwi = t / 'wmparcInDwi.nii.gz'
ConvertBetweenFileFormats(self.fsindwi, fsindwi)
if '.gz' in self.ukf.suffix:
ukf = t / 'ukf.vtk'
from plumbum.cmd import gunzip
(gunzip['-c', self.ukf] > ukf)()
tract_querier = local['tract_querier']
tract_math = local['tract_math']
ukfpruned = t / 'ukfpruned.vtk'
# tract_math(ukf, 'tract_remove_short_tracts', '2', ukfpruned)
tract_math[ukf, 'tract_remove_short_tracts', '2', ukfpruned] & FG
if not ukfpruned.exists():
raise Exception(
"tract_math failed to make '{}'".format(ukfpruned))
self.out.mkdir()
tract_querier['-t', ukfpruned, '-a', fsindwi, '-q', self.query,
'-o', self.out / '_'] & FG
logging.info('Convert vtk field data to tensor data')
# use the following multi-processed loop
pool = Pool(int(self.nproc))
pool.map_async(_activateTensors_py, self.out.glob('*.vtk'))
pool.close()
pool.join()
def main(self):
with TemporaryDirectory() as t:
t = local.path(t)
ukf = self.ukf
fsindwi = self.fsindwi
if nrrd(self.fsindwi):
fsindwi = t / 'wmparcInDwi.nii.gz'
ConvertBetweenFileFormats(self.fsindwi, fsindwi)
if '.gz' in self.ukf.suffix:
ukf = t / 'ukf.vtk'
from plumbum.cmd import gunzip
(gunzip['-c', self.ukf] > ukf)()
tract_querier = local['tract_querier']
tract_math = local['tract_math']
ukfpruned = t / 'ukfpruned.vtk'
# tract_math(ukf, 'tract_remove_short_tracts', '2', ukfpruned)
tract_math[ukf, 'tract_remove_short_tracts', '2', ukfpruned] & FG
if not ukfpruned.exists():
raise Exception(
"tract_math failed to make '{}'".format(ukfpruned))
self.out.mkdir()
tract_querier['-t', ukfpruned, '-a', fsindwi, '-q', self.query,
'-o', self.out / '_'] & FG
logging.info('Convert vtk field data to tensor data')
for vtk in self.out.glob('*.vtk'):
vtknew = vtk.dirname / (vtk.stem[2:] + ''.join(vtk.suffixes))
activateTensors_py(vtk, vtknew)
vtk.delete()
def makeAtlases(target, trainingTable, outdir, mabs=False):
outdir = local.path(outdir)
from plumbum.cmd import mkdir
mkdir('-p', outdir)
logging.info(
'Create atlases: compute transforms from images to target and apply')
for idx, r in trainingTable.iterrows():
warp = outdir / 'warp{idx}.nii.gz'.format(**locals())
atlas = outdir / 'atlas{idx}.nii.gz'.format(**locals())
computeWarp(r['image'], target, warp)
applyWarp(r['image'], warp, target, atlas)
for labelname, label in r.iloc[1:].iteritems():
atlaslabel = outdir / '{labelname}{idx}.nii.gz'.format(**locals())
applyWarp(label,
warp,
target,
atlaslabel,
interpolation='NearestNeighbor')
if mabs:
from plumbum.cmd import unu, ConvertBetweenFileFormats, AverageImages
for labelname in list(trainingTable)[1:]:
out = outdir / labelname + '.nrrd'
labelmaps = outdir // labelname + '*'
with TemporaryDirectory() as tmpdir:
nii = tmpdir / 'mabs.nii.gz'
AverageImages('3', nii, '0', *labelmaps)
ConvertBetweenFileFormats(nii, out)
unu['2op', 'gt', out, '0.5'] | \
unu['save', '-e', 'gzip', '-f', 'nrrd', '-o', out] & FG
def fuseAvg(labels, out):
from plumbum.cmd import AverageImages
with local.tempdir() as tmpdir:
nii = local.path(tmpdir) / 'avg.nii.gz'
AverageImages('3', nii, '0', *labels)
ConvertBetweenFileFormats(nii, out)
(unu['2op', 'gt', out, '0.5'] | \
unu['save', '-e', 'gzip', '-f', 'nrrd', '-o', out]) & FG
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 fuseAvg(labels, out):
from plumbum.cmd import AverageImages
with local.tempdir() as tmpdir:
nii = local.path(tmpdir) / 'avg.nii.gz'
AverageImages('3', nii, '0', *labels)
# out is {labelname}.nrrd
ConvertBetweenFileFormats(nii, out)
# Binary operation, if out>0.5, pipe the output and save as {labelname}.nrrd
(unu['2op', 'gt', out, '0.5'] | \
unu['save', '-e', 'gzip', '-f', 'nrrd', '-o', out]) & FG
def main(self):
fshome = local.path(os.getenv('FREESURFER_HOME'))
if not fshome:
logging.error('Set FREESURFER_HOME first.')
sys.exit(1)
if not self.force and self.out.exists():
logging.error(
'Output directory exists, use -f/--force to force an overwrite.'
)
sys.exit(1)
with TemporaryDirectory() as tmpdir, local.env(SUBJECTS_DIR=tmpdir,
FSFAST_HOME='',
MNI_DIR=''):
if self.t1mask:
logging.info('Mask the t1')
ImageMath('3', tmpdir / 't1masked.nii.gz', 'm', self.t1,
self.t1mask)
t1 = tmpdir / 't1masked.nii.gz'
skullstrip = '-noskullstrip'
else:
skullstrip = ''
if '.nrrd' in self.t1.suffixes or '.nhdr' in self.t1.suffixes:
logging.info('t1 is in nrrd format, convert to nifti')
t1 = tmpdir / 't1.nii.gz'
ConvertBetweenFileFormats(self.t1, t1)
logging.info("Run freesurfer on " + t1)
subjid = t1.stem
from plumbum.cmd import bash
bash['-c',
'source ' + fshome + '/FreeSurferEnv.sh; recon-all -s ' +
subjid + ' -i ' + t1 + ' -autorecon1 ' + skullstrip] & FG
(tmpdir / subjid / 'mri/T1.mgz').copy(tmpdir / subjid /
'mri/brainmask.mgz')
bash['-c', 'source ' + fshome +
'/FreeSurferEnv.sh; recon-all -autorecon2 -subjid ' +
subjid] & FG
bash['-c', 'source ' + fshome +
'/FreeSurferEnv.sh; recon-all -autorecon3 -subjid ' +
subjid] & FG
logging.info("Freesurfer done.")
(tmpdir / subjid).copy(self.out,
override=True) # overwrites existing
logging.info("Made " + self.out)
def fuseWeightedAvg(labels, weights, out):
# for each label, fuse warped labelmaps to compute output labelmap
print("Apply weights to warped training {} et al., fuse, and threshold".format(labels[0]))
init= True
for label, w in zip(labels, weights):
img= nib.load(str(label))
if init:
data=img.get_data()*w
affine= img.affine
init= False
else:
data+=img.get_data()*w
data= (data>0.5)*1
with TemporaryDirectory() as tmpdir:
nii = local.path(tmpdir) / 'avg.nii.gz'
Nifti1Image= nib.Nifti1Image(data, affine= affine, header= img.header)
nib.save(Nifti1Image, str(nii))
ConvertBetweenFileFormats(nii, out)
print("Made labelmap: " + out)
def convertImage(i, o, bthash):
if i.suffixes == o.suffixes:
i.copy(o)
with BRAINSTools.env(bthash):
from plumbum.cmd import ConvertBetweenFileFormats
ConvertBetweenFileFormats(i, o)
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()))
def main(self):
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
b0masked = tmpdir / "b0masked.nii.gz" # Sylvain wants both
b0maskedbrain = tmpdir / "b0maskedbrain.nii.gz"
t2masked = tmpdir / 't2masked.nii.gz'
logging.info('Masking the T2')
ImageMath(3, t2masked, 'm', self.t2, self.t2mask)
brain = tmpdir / "brain.nii.gz"
wmparc = tmpdir / "wmparc.nii.gz"
brainmgz = self.parent.fsdir / 'mri/brain.mgz'
wmparcmgz = self.parent.fsdir / 'mri/wmparc.mgz'
wmparcindwi = tmpdir / 'wmparcInDwi.nii.gz' # Sylvain wants both
wmparcinbrain = tmpdir / 'wmparcInBrain.nii.gz'
logging.info(
"Making brain.nii.gz and wmparc.nii.gz from their mgz versions"
)
vol2vol = local[self.parent.fshome / 'bin/mri_vol2vol']
label2vol = local[self.parent.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('Extracting B0 from DWI and masking it')
bse_py['-i', self.parent.dwi, '-m', self.parent.dwimask, '-o',
tmpdir / 'b0mask.nrrd'] & FG
ConvertBetweenFileFormats(tmpdir / 'b0mask.nrrd', b0masked)
logging.info('Made masked B0')
# rigid registration from t2 to brain.nii.gz
pre = tmpdir / 'BrainToT2'
BrainToT2Affine = pre + '0GenericAffine.mat'
logging.info(
'Computing rigid registration from brain.nii.gz to t2')
# antsRegistrationSyNMI_sh['-d', '3', '-t', 'r', '-m', brain, '-f', t2masked, '-o', pre,
# '-n', N_CPU] & FG
rigid_registration(3, brain, t2masked, pre)
# generates three files for rigid registration:
# pre0GenericAffine.mat preInverseWarped.nii.gz preWarped.nii.gz
# generates five files for default(rigid+affine+deformable syn) registration:
# pre0GenericAffine.mat pre1Warp.nii.gz preWarped.nii.gz pre1InverseWarp.nii.gz preInverseWarped.nii.gz
dwi_res = nib.load(str(b0masked)).header['pixdim'][1:4].round()
brain_res = nib.load(str(brain)).header['pixdim'][1:4].round()
logging.info(f'DWI resolution: {dwi_res}')
logging.info(f'FreeSurfer brain resolution: {brain_res}')
if dwi_res.ptp() or brain_res.ptp():
logging.info('Resolution is not uniform among all the axes')
logging.info('Registering wmparc to B0 through T2')
registerFs2Dwi_T2(tmpdir, 'fsbrainToT2ToB0', b0masked, t2masked,
BrainToT2Affine, wmparc, wmparcindwi)
if (dwi_res != brain_res).any():
logging.info(
'DWI resolution is different from FreeSurfer brain resolution'
)
logging.info(
'wmparc wil be registered to both DWI and brain resolution'
)
logging.info(
'Check output files wmparcInDwi.nii.gz and wmparcInBrain.nii.gz'
)
logging.info('Resampling B0 to brain resolution')
ResampleImageBySpacing('3', b0masked, b0maskedbrain,
brain_res.tolist())
logging.info('Registering wmparc to resampled B0')
registerFs2Dwi_T2(tmpdir, 'fsbrainToT2ToResampledB0',
b0maskedbrain, t2masked, BrainToT2Affine,
wmparc, wmparcinbrain)
# copying images to outDir
b0masked.copy(self.parent.out)
wmparcindwi.copy(self.parent.out)
if b0maskedbrain.exists():
b0maskedbrain.copy(self.parent.out)
wmparcinbrain.copy(self.parent.out)
if self.parent.debug:
tmpdir.copy(self.parent.out,
'fs2dwi-debug-' + str(os.getpid()))
logging.info('See output files in ' + self.parent.out._path)
def main(self):
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
b0masked = tmpdir / "b0masked.nii.gz" # Sylvain wants both
b0maskedbrain = tmpdir / "b0maskedbrain.nii.gz"
brain = tmpdir / "brain.nii.gz"
wmparc = tmpdir / "wmparc.nii.gz"
brainmgz = self.parent.fsdir / 'mri/brain.mgz'
wmparcmgz = self.parent.fsdir / 'mri/wmparc.mgz'
wmparcindwi = tmpdir / 'wmparcInDwi.nii.gz' # Sylvain wants both
wmparcinbrain = tmpdir / 'wmparcInBrain.nii.gz'
logging.info(
"Making brain.nii.gz and wmparc.nii.gz from their mgz versions"
)
vol2vol = local[self.parent.fshome / 'bin/mri_vol2vol']
label2vol = local[self.parent.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('Extracting B0 from DWI and masking it')
bse_py['-i', self.parent.dwi, '-m', self.parent.dwimask, '-o',
tmpdir / 'b0mask.nrrd'] & FG
ConvertBetweenFileFormats(tmpdir / 'b0mask.nrrd', b0masked)
logging.info('Made masked B0')
dwi_res = nib.load(str(b0masked)).header['pixdim'][1:4].round()
brain_res = nib.load(str(brain)).header['pixdim'][1:4].round()
logging.info(f'DWI resolution: {dwi_res}')
logging.info(f'FreeSurfer brain resolution: {brain_res}')
if dwi_res.ptp() or brain_res.ptp():
logging.info('Resolution is not uniform among all the axes')
logging.info('Registering wmparc to B0')
registerFs2Dwi(tmpdir, 'fsbrainToB0', b0masked, brain, wmparc,
wmparcindwi)
if (dwi_res != brain_res).any():
logging.info(
'DWI resolution is different from FreeSurfer brain resolution'
)
logging.info(
'wmparc wil be registered to both DWI and brain resolution'
)
logging.info(
'Check output files wmparcInDwi.nii.gz and wmparcInBrain.nii.gz'
)
logging.info('Resampling B0 to brain resolution')
ResampleImageBySpacing('3', b0masked, b0maskedbrain,
brain_res.tolist())
logging.info('Registering wmparc to resampled B0')
registerFs2Dwi(tmpdir, 'fsbrainToResampledB0', b0maskedbrain,
brain, wmparc, wmparcinbrain)
# copying images to outDir
b0masked.copy(self.parent.out)
wmparcindwi.copy(self.parent.out)
if b0maskedbrain.exists():
b0maskedbrain.copy(self.parent.out)
wmparcinbrain.copy(self.parent.out)
if self.parent.debug:
tmpdir.copy(self.parent.out,
'fs2dwi-debug-' + str(os.getpid()))
logging.info('See output files in ' + self.parent.out._path)