def main(self):
prefix = self.dwi_file.name.split('.')[0]
outPrefix = pjoin(self.outDir._path, prefix + '_Ed')
if self.b0_brain_mask == 'None':
logging.info('Mask not provided, creating mask ...')
self.b0_brain_mask = outPrefix + '_mask.nii.gz'
bet_mask(self.dwi_file,
self.b0_brain_mask,
4,
bvalFile=self.bvals_file,
BET_THRESHOLD=self.betThreshold)
eddy_openmp[f'--imain={self.dwi_file}', f'--mask={self.b0_brain_mask}',
f'--acqp={self.acqparams_file}',
f'--index={self.index_file}', f'--bvecs={self.bvecs_file}',
f'--bvals={self.bvals_file}', f'--out={outPrefix}',
'--verbose',
eddy_openmp_params.split()] & FG
# copy bval,bvec to have same prefix as that of eddy corrected volume
copyfile(outPrefix + '.eddy_rotated_bvecs', outPrefix + '.bvec')
copyfile(self.bvals_file, outPrefix + '.bval')
def main(self):
if not self.b0_brain_mask:
logging.info('Mask not provided, creating mask ...')
self.b0_brain_mask = self.outPrefix + '_mask.nii.gz'
bet_mask(self.dwi_file,
self.b0_brain_mask,
dim=4,
bvalFile=self.bvals_file,
BET_THRESHOLD=self.betThreshold)
_, _, eddy_openmp_params = obtain_fsl_eddy_params(
self.eddy_config_file._path)
eddy_openmp[f'--imain={self.dwi_file}', f'--mask={self.b0_brain_mask}',
f'--acqp={self.acqparams_file}',
f'--index={self.index_file}', f'--bvecs={self.bvecs_file}',
f'--bvals={self.bvals_file}', f'--out={self.outPrefix}',
'--verbose',
eddy_openmp_params.split()] & FG
# copy bval,bvec to have same prefix as that of eddy corrected volume
copyfile(self.outPrefix + '.eddy_rotated_bvecs',
self.outPrefix + '.bvec')
copyfile(self.bvals_file, self.outPrefix + '.bval')
def main(self):
from plumbum.cmd import eddy_openmp
if self.useGpu:
try:
from plumbum.cmd import nvcc
nvcc['--version'] & FG
print('\nCUDA found, looking for available GPU\n')
from GPUtil import getFirstAvailable
getFirstAvailable()
print('available GPU found, looking for eddy_cuda executable\n'
'make sure you have created a softlink according to '
'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide')
from plumbum.cmd import eddy_cuda as eddy_openmp
print('\neddy_cuda executable found\n')
except:
print(
'nvcc, available GPU, and/or eddy_cuda was not found, using eddy_openmp'
)
prefix = self.dwi_file.name.split('.')[0]
self.outDir.mkdir()
outPrefix = pjoin(self.outDir._path, prefix + '_Ed')
if not self.b0_brain_mask:
logging.info('Mask not provided, creating mask ...')
self.b0_brain_mask = outPrefix + '_mask.nii.gz'
bet_mask(self.dwi_file,
self.b0_brain_mask,
4,
bvalFile=self.bvals_file,
BET_THRESHOLD=self.betThreshold)
_, _, eddy_openmp_params = obtain_fsl_eddy_params(
self.eddy_config_file._path)
print('eddy_openmp/cuda parameters')
print(eddy_openmp_params)
print('')
eddy_openmp[f'--imain={self.dwi_file}', f'--mask={self.b0_brain_mask}',
f'--acqp={self.acqparams_file}',
f'--index={self.index_file}', f'--bvecs={self.bvecs_file}',
f'--bvals={self.bvals_file}', f'--out={outPrefix}',
eddy_openmp_params.split()] & FG
# free space, see https://github.com/pnlbwh/pnlNipype/issues/82
if '--repol' in eddy_openmp_params:
rm[f'{outPrefix}.eddy_outlier_free_data.nii.gz'] & FG
bvals = np.array(read_bvals(self.bvals_file))
ind = [
i for i in range(len(bvals))
if bvals[i] > B0_THRESHOLD and bvals[i] <= REPOL_BSHELL_GREATER
]
if '--repol' in eddy_openmp_params and len(ind):
print(
'\nDoing eddy_openmp/cuda again without --repol option '
'to obtain eddy correction w/o outlier replacement for b<=500 shells\n'
)
eddy_openmp_params = eddy_openmp_params.split()
eddy_openmp_params.remove('--repol')
print(eddy_openmp_params)
print('')
wo_repol_outDir = self.outDir.join('wo_repol')
wo_repol_outDir.mkdir()
wo_repol_outPrefix = pjoin(wo_repol_outDir, prefix + '_Ed')
eddy_openmp[
f'--imain={self.dwi_file}', f'--mask={self.b0_brain_mask}',
f'--acqp={self.acqparams_file}', f'--index={self.index_file}',
f'--bvecs={self.bvecs_file}', f'--bvals={self.bvals_file}',
f'--out={wo_repol_outPrefix}', eddy_openmp_params] & FG
repol_bvecs = np.array(
read_bvecs(outPrefix + '.eddy_rotated_bvecs'))
wo_repol_bvecs = np.array(
read_bvecs(wo_repol_outPrefix + '.eddy_rotated_bvecs'))
merged_bvecs = repol_bvecs.copy()
merged_bvecs[ind, :] = wo_repol_bvecs[ind, :]
repol_data = load_nifti(outPrefix + '.nii.gz')
wo_repol_data = load_nifti(wo_repol_outPrefix + '.nii.gz')
merged_data = repol_data.get_fdata().copy()
merged_data[..., ind] = wo_repol_data.get_fdata()[..., ind]
save_nifti(outPrefix + '.nii.gz',
merged_data,
repol_data.affine,
hdr=repol_data.header)
# copy bval,bvec to have same prefix as that of eddy corrected volume
write_bvecs(outPrefix + '.bvec', merged_bvecs)
copyfile(self.bvals_file, outPrefix + '.bval')
# clean up
rm['-r', wo_repol_outDir] & FG
else:
# copy bval,bvec to have same prefix as that of eddy corrected volume
copyfile(outPrefix + '.eddy_rotated_bvecs', outPrefix + '.bvec')
copyfile(self.bvals_file, outPrefix + '.bval')