def main(self):
if isNifti(self.dwi):
fsl_extract_b0(self.dwi, self.out)
elif isNrrd(self.dwi):
nrrd_extract_b0(self.dwi, self.out)
else:
raise Exception("Invalid dwi format, must be nrrd or nifti")
if self.dwimask:
from plumbum.cmd import ImageMath
ImageMath(3, self.out, 'm', self.out, self.dwimask)
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 main(self):
prefix = self.dwi.name.split('.')[0]
directory = self.dwi.parent
self.b0_threshold = float(self.b0_threshold)
if self.out is None:
self.out = os.path.join(directory, prefix + '_bse.nii.gz')
if self.dwi.endswith('.nii') or self.dwi.endswith('.nii.gz'):
if not self.bval_file:
self.bval_file = os.path.join(directory, prefix + '.bval')
bvals = read_bvals(self.bval_file)
idx = np.where([bval < self.b0_threshold for bval in bvals])[0]
if len(idx) > 1:
# default is the first b0
if not (self.minimum or self.average or self.all):
fslroi[self.dwi, self.out, idx, 1] & FG
elif self.minimum:
fslroi[self.dwi, self.out, idx, np.argsort(bvals)[0]] & FG
elif self.average:
# Load the given dwi to get image data
dwi = load_nifti(self.dwi._path)
hdr = dwi.header
mri = dwi.get_data()
avg_bse = np.mean(mri[:, :, :, idx], axis=3)
# Now write back the average bse
save_nifti(self.out, avg_bse, dwi.affine, hdr)
elif self.all:
fslroi[self.dwi, self.out, idx, len(idx)] & FG
else:
raise Exception('No b0 image found. Check the bval file.')
else:
raise Exception("Invalid dwi format, must be a nifti image")
if self.dwimask:
ImageMath(3, self.out, 'm', self.out, self.dwimask)
def main(self):
with tempfile.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'
print('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'
print(
"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)
print('Extracting B0 from DWI and masking it')
check_call((' ').join([
pjoin(FILEDIR, 'bse.py'), '-i', self.parent.dwi, '-m',
self.parent.dwimask, '-o', b0masked
]),
shell=True)
print('Made masked B0')
# rigid registration from t2 to brain.nii.gz
pre = tmpdir / 'BrainToT2'
BrainToT2Affine = pre + '0GenericAffine.mat'
print('Computing rigid registration from brain.nii.gz to t2')
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 = load_nifti(
str(b0masked)).header['pixdim'][1:4].round(decimals=2)
brain_res = load_nifti(
str(brain)).header['pixdim'][1:4].round(decimals=2)
print(f'DWI resolution: {dwi_res}')
print(f'FreeSurfer brain resolution: {brain_res}')
print('Registering wmparc to B0 through T2')
registerFs2Dwi_T2(tmpdir, 'fsbrainToT2ToB0', b0masked, t2masked,
BrainToT2Affine, wmparc, wmparcindwi)
if (dwi_res != brain_res).any():
print(
'DWI resolution is different from FreeSurfer brain resolution'
)
print(
'wmparc wil be registered to both DWI and brain resolution'
)
print(
'Check output files wmparcInDwi.nii.gz and wmparcInBrain.nii.gz'
)
print('Resampling B0 to brain resolution')
ResampleImageBySpacing('3', b0masked, b0maskedbrain,
brain_res.tolist())
print('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()))
print('See output files in ', self.parent.out._path)
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 os.path.exists(self.out):
logging.error(
'Output directory exists, use -f/--force to force an overwrite.'
)
sys.exit(1)
if self.t2mask and not self.t2:
raise AttributeError('--t2mask is invalid without --t2')
with TemporaryDirectory() as tmpdir, local.env(SUBJECTS_DIR=tmpdir,
FSFAST_HOME='',
MNI_DIR=''):
tmpdir = local.path(tmpdir)
if self.t1mask:
logging.info('Mask the t1')
t1 = tmpdir / 't1masked.nii.gz'
ImageMath('3', t1, 'm', self.t1, self.t1mask)
else:
t1 = tmpdir / 't1.nii.gz'
self.t1.copy(t1)
subjid = self.t1.stem
common_params = ['-s', subjid]
autorecon3_params = []
if self.t2:
if self.t2mask:
logging.info('Mask the t2')
t2 = tmpdir / 't2masked.nii.gz'
ImageMath('3', t2, 'm', self.t2, self.t2mask)
else:
t2 = tmpdir / 't2.nii.gz'
self.t2.copy(t2)
autorecon3_params = ['-T2', t2, '-T2pial']
if self.subfields:
autorecon3_params += ['-subfields']
logging.info("Running freesurfer on " + t1)
if self.ncpu == '-1':
self.ncpu = str(N_CPU)
if int(self.ncpu) > 1:
common_params += ['-parallel', '-openmp', self.ncpu]
autorecon1_params = []
if not self.no_hires:
common_params.append('-hires')
autorecon1_params = ['-expert', self.expert_file]
if self.no_rand:
common_params.append('-norandomness')
# run recon_all in three steps so we can overwrite/provide MABS masked T1
# -noskullstrip is used with -autorecon1 only, so we need to check whether T1 is masked/T1 mask is provided
# irrespective of masked/unmasked T2
if self.t1mask or self.no_skullstrip:
recon_all['-i', t1, common_params, '-autorecon1',
autorecon1_params, '-noskullstrip'] & FG
(tmpdir / subjid / 'mri/T1.mgz').copy(tmpdir / subjid /
'mri/brainmask.mgz')
else:
recon_all['-i', t1, common_params, '-autorecon1',
autorecon1_params] & FG
recon_all[common_params, '-autorecon2'] & FG
recon_all[common_params, '-autorecon3', autorecon3_params] & FG
logging.info("Freesurfer done.")
(tmpdir / subjid).copy(
self.out, override=True) # overwrites any existing directory
logging.info("Made " + self.out)
def main(self):
ImageMath(self.dim, self.out, 'm', self.img, self.mask)
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 os.path.exists(self.out):
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')
t1 = tmpdir / 't1masked.nii.gz'
ImageMath('3', t1, 'm', self.t1, self.t1mask)
skullstrip = '-noskullstrip'
else:
skullstrip = '-skullstrip'
t1 = tmpdir / 't1.nii.gz'
self.t1.copy(t1)
if self.t2mask:
logging.info('Mask the t2')
t2 = tmpdir / 't2masked.nii.gz'
ImageMath('3', t2, 'm', self.t2, self.t2mask)
skullstrip = '-noskullstrip'
else:
skullstrip = '-skullstrip'
t2 = tmpdir / 't2.nii.gz'
self.t2.copy(t2)
logging.info("Run freesurfer on " + t1)
subjid = t1.stem
if self.ncpu == '-1':
self.ncpu = N_CPU
if int(self.ncpu) > 1:
if self.t2:
bash['-c', 'recon-all -s ' + subjid + ' -i ' + t1 +
' -T2 ' + t2 + ' -autorecon1 ' + skullstrip +
' -parallel -openmp ' + self.ncpu] & FG
else:
bash['-c', 'recon-all -s ' + subjid + ' -i ' + t1 +
' -autorecon1 ' + skullstrip + ' -parallel -openmp ' +
self.ncpu] & FG
(tmpdir / subjid / 'mri/T1.mgz').copy(tmpdir / subjid /
'mri/brainmask.mgz')
bash['-c', 'recon-all -autorecon2 -subjid ' + subjid +
' -parallel -openmp ' + self.ncpu] & FG
bash['-c', 'recon-all -autorecon3 -subjid ' + subjid +
' -parallel -openmp ' + self.ncpu] & FG
else: # intentionally writing a separate block omitting parallelization attributes
if self.t2:
bash['-c', 'recon-all -s ' + subjid + ' -i ' + t1 +
' -T2 ' + t2 + ' -autorecon1 ' + skullstrip] & FG
else:
bash['-c', 'recon-all -s ' + subjid + ' -i ' + t1 +
' -autorecon1 ' + skullstrip] & FG
(tmpdir / subjid / 'mri/T1.mgz').copy(tmpdir / subjid /
'mri/brainmask.mgz')
bash['-c', 'recon-all -autorecon2 -subjid ' + subjid] & FG
bash['-c', 'recon-all -autorecon3 -subjid ' + subjid] & FG
logging.info("Freesurfer done.")
(tmpdir / subjid).copy(
self.out, override=True) # overwrites any existing directory
logging.info("Made " + self.out)