def main(self):
# if self.force:
# logging.info('Deleting previous output directory')
# rm('-rf', self.outDir)
temp= self.dwi_file.split(',')
primaryVol= abspath(temp[0])
if len(temp)<2:
raise AttributeError('Two volumes are required for --imain')
else:
secondaryVol= abspath(temp[1])
if self.b0_brain_mask:
temp = self.b0_brain_mask.split(',')
primaryMask = abspath(temp[0])
if len(temp) == 2:
secondaryMask = abspath(temp[1])
else:
secondaryMask = abspath(temp[0])
else:
primaryMask=[]
secondaryMask=[]
# obtain 4D/3D info and time axis info
dimension = load_nifti(primaryVol).header['dim']
dim1 = dimension[0]
if dim1!=4:
raise AttributeError('primary volume must be 4D, however, secondary can be 3D/4D')
numVol1 = dimension[4]
dimension = load_nifti(secondaryVol).header['dim']
dim2 = dimension[0]
numVol2 = dimension[4]
temp= self.bvals_file.split(',')
if len(temp)>=1:
primaryBval= abspath(temp[0])
if len(temp)==2:
secondaryBval= abspath(temp[1])
elif len(temp)==1 and dim2==4:
secondaryBval= primaryBval
elif len(temp)==1 and dim2==3:
secondaryBval=[]
elif len(temp)==0:
raise AttributeError('--bvals are required')
temp= self.bvecs_file.split(',')
if len(temp)>=1:
primaryBvec= abspath(temp[0])
if len(temp)==2:
secondaryBvec= abspath(temp[1])
elif len(temp) == 1 and dim2 == 4:
secondaryBvec = primaryBvec
elif len(temp)==1 and dim2==3:
secondaryBvec=[]
else:
raise AttributeError('--bvecs are required')
with TemporaryDirectory() as tmpdir:
tmpdir= local.path(tmpdir)
# mask both volumes, fslmaths can do that irrespective of dimension
logging.info('Masking the volumes')
primaryMaskedVol = tmpdir / 'primaryMasked.nii.gz'
secondaryMaskedVol = tmpdir / 'secondaryMasked.nii.gz'
if primaryMask:
# mask the volume
fslmaths[primaryVol, '-mas', primaryMask, primaryMaskedVol] & FG
else:
primaryMaskedVol= primaryVol
if secondaryMask:
# mask the volume
fslmaths[secondaryVol, '-mas', secondaryMask, secondaryMaskedVol] & FG
else:
secondaryMaskedVol= secondaryVol
logging.info('Extracting B0 from masked volumes')
B0_PA= tmpdir / 'B0_PA.nii.gz'
B0_AP= tmpdir / 'B0_AP.nii.gz'
obtainB0(primaryMaskedVol, primaryBval, B0_PA, self.num_b0)
if dim2==4:
obtainB0(secondaryMaskedVol, secondaryBval, B0_AP, self.num_b0)
else:
B0_AP= secondaryMaskedVol
B0_PA_AP_merged = tmpdir / 'B0_PA_AP_merged.nii.gz'
with open(self.acqparams_file._path) as f:
acqp= f.read().split('\n')
logging.info('Writing acqparams.txt for topup')
# firstDim: first acqp line should be replicated this number of times
firstB0dim= load_nifti(str(B0_PA)).header['dim'][4]
# secondDim: second acqp line should be replicated this number of times
secondB0dim= load_nifti(str(B0_AP)).header['dim'][4]
acqp_topup= tmpdir / 'acqp_topup.txt'
with open(acqp_topup,'w') as f:
for i in range(firstB0dim):
f.write(acqp[0]+'\n')
for i in range(secondB0dim):
f.write(acqp[1]+'\n')
logging.info('Merging B0_PA and BO_AP')
fslmerge('-t', B0_PA_AP_merged, B0_PA, B0_AP)
topup_params, applytopup_params, eddy_openmp_params= obtain_fsl_eddy_params(self.eddy_config_file._path)
# Example for topup
# === on merged b0 images ===
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#Running_topup_on_the_b.3D0_volumes
# topup --imain=both_b0 --datain=my_acq_param.txt --out=my_topup_results
# === on all b0 images ===
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Running_topup
# topup --imain=all_my_b0_images.nii --datain=acquisition_parameters.txt --config=b02b0.cnf --out=my_output
logging.info('Running topup')
topup_results= tmpdir / 'topup_results'
topup[f'--imain={B0_PA_AP_merged}',
f'--datain={acqp_topup}',
f'--out={topup_results}',
'--verbose',
topup_params.split()] & FG
logging.info('Running applytopup')
topupMask= tmpdir / 'topup_mask.nii.gz'
# applytopup on primary4D,secondary4D/3D
topupOut= tmpdir / 'topup_out.nii.gz'
if dim2==4:
applytopup[f'--imain={primaryMaskedVol},{secondaryMaskedVol}',
f'--datain={self.acqparams_file}',
'--inindex=1,2',
f'--topup={topup_results}',
f'--out={topupOut}',
'--verbose',
applytopup_params.split()] & FG
else:
applytopup[f'--imain={B0_PA},{B0_AP}',
f'--datain={self.acqparams_file}',
'--inindex=1,2',
f'--topup={topup_results}',
f'--out={topupOut}',
'--verbose',
applytopup_params.split()] & FG
topupOutMean= tmpdir / 'topup_out_mean.nii.gz'
fslmaths[topupOut, '-Tmean', topupOutMean] & FG
bet[topupOutMean, topupMask._path.split('_mask.nii.gz')[0], '-m', '-n'] & FG
# another approach could be
# threshold mean of primary,secondary mask at 0.5 and obtain modified mask, use that mask for eddy_openmp
# fslmerge[topupMask, '-t', primaryMask, secondaryMask] & FG
# fslmaths[topupMask, '-Tmean', topupMask] & FG
# fslmaths[topupMask, '-thr', '0.5', topupMask, '-odt' 'char'] & FG
logging.info('Writing index.txt for topup')
indexFile= tmpdir / 'index.txt'
with open(indexFile, 'w') as f:
for i in range(numVol1):
f.write('1\n')
outPrefix = tmpdir / basename(primaryVol).split('.')[0] + '_Ep_Ed'
temp = self.whichVol.split(',')
if len(temp)==1 and temp[0]=='1':
# correct only primary4D volume
eddy_openmp[f'--imain={primaryMaskedVol}',
f'--mask={topupMask}',
f'--acqp={self.acqparams_file}',
f'--index={indexFile}',
f'--bvecs={primaryBvec}',
f'--bvals={primaryBval}',
f'--out={outPrefix}',
f'--topup={topup_results}',
'--verbose',
eddy_openmp_params.split()] & FG
elif len(temp)==2 and temp[1]=='2':
# sylvain would like to correct both primary and secondary volumes
with open(indexFile, 'a') as f:
for i in range(numVol2):
f.write('2\n')
# join both bvalFiles
bvals1= read_bvals(primaryBval)
if dim2==4 and not secondaryBval:
bvals2= bvals1.copy()
elif dim2==4 and secondaryBval:
bvals2= read_bvals(secondaryBval)
elif dim2==3:
bvals2=[0]
combinedBvals = tmpdir / 'combinedBvals.txt'
write_bvals(combinedBvals, bvals1+bvals2)
# join both bvecFiles
bvecs1= read_bvecs(primaryBvec)
if dim2==4 and not secondaryBvec:
bvecs2= bvecs1.copy()
elif dim2==4 and secondaryBvec:
bvecs2= read_bvecs(secondaryBvec)
elif dim2==3:
bvecs2=[[0,0,0]]
# join both bvecFiles
combinedBvecs = tmpdir / 'combinedBvecs.txt'
write_bvecs(combinedBvecs, bvecs1+bvecs2)
combinedData= tmpdir / 'combinedData.nii.gz'
fslmerge('-t', combinedData, primaryMaskedVol, secondaryMaskedVol)
eddy_openmp[f'--imain={combinedData}',
f'--mask={topupMask}',
f'--acqp={self.acqparams_file}',
f'--index={indexFile}',
f'--bvecs={combinedBvecs}',
f'--bvals={combinedBvals}',
f'--out={outPrefix}',
f'--topup={topup_results}',
'--verbose',
eddy_openmp_params.split()] & FG
else:
raise ValueError('Invalid --whichVol')
# copy bval,bvec to have same prefix as that of eddy corrected volume
copyfile(outPrefix+'.eddy_rotated_bvecs', outPrefix+'.bvec')
copyfile(primaryBval, outPrefix+'.bval')
# rename topupMask to have same prefix as that of eddy corrected volume
topupMask.move(outPrefix+'_mask.nii.gz')
tmpdir.move(self.outDir)
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):
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)
dicePrefix = 'vol'
logging.info('Dice the DWI')
fslsplit[self.dwi] & FG
logging.info('Extract the B0')
check_call((' ').join([pjoin(FILEDIR,'bse.py'), '-i', self.dwi._path, '-o', 'b0.nii.gz']), shell= True)
logging.info('Register each volume to the B0')
vols = sorted(tmpdir // (dicePrefix + '*.nii.gz'))
# 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')
# 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.nii.gz', volsRegistered)
transforms = tmpdir.glob(dicePrefix+'*.txt')
transforms.sort()
logging.info('Extract the rotations and realign the gradients')
bvecs= read_bvecs(self.bvecFile._path)
bvecs_new= bvecs.copy()
for (i,t) in enumerate(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
# 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
bvecs_new[i] = np.dot(rot,bvecs[i]).tolist()[0]
tar('cvzf', outxfms, transforms)
# save modified bvecs
write_bvecs(self.out._path+'.bvec', bvecs_new)
# save EddyCorrect-DWI
local.path('EddyCorrect-DWI.nii.gz').copy(self.out._path+'.nii.gz')
# copy bvals
self.bvalFile.copy(self.out._path+'.bval')
if self.debug:
tmpdir.copy(pjoin(dirname(self.out),"eddy-debug-"+str(getpid())))
def main(self):
from plumbum.cmd import eddy_openmp
# cli.NonexistentPath is already making sure it does not exist
self.outDir.mkdir()
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')
def _eddy_openmp(modData, modBvals, modBvecs, eddy_openmp_params):
print('eddy_openmp/cuda parameters')
print(eddy_openmp_params)
print('')
# eddy_openmp yields as many volumes as there are input volumes
# this is the main output and consists of the input data after correction for
# eddy currents, subject movement, and susceptibility if --topup was specified
eddy_openmp[f'--imain={modData}',
f'--mask={topupMask}',
f'--acqp={self.acqparams_file}',
f'--index={indexFile}',
f'--bvecs={modBvecs}',
f'--bvals={modBvals}',
f'--out={outPrefix}',
f'--topup={topup_results}',
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(modBvals))
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 '
f'to obtain eddy correction w/o outlier replacement for b<={REPOL_BSHELL_GREATER} shells\n')
eddy_openmp_params = eddy_openmp_params.split()
eddy_openmp_params.remove('--repol')
print(eddy_openmp_params)
print('')
wo_repol_outDir = local.path(outPrefix).dirname.join('wo_repol')
wo_repol_outDir.mkdir()
wo_repol_outPrefix = pjoin(wo_repol_outDir, basename(outPrefix))
eddy_openmp[f'--imain={modData}',
f'--mask={topupMask}',
f'--acqp={self.acqparams_file}',
f'--index={indexFile}',
f'--bvecs={modBvecs}',
f'--bvals={modBvals}',
f'--out={wo_repol_outPrefix}',
f'--topup={topup_results}',
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(modBvals, 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(modBvals, outPrefix + '.bval')
# if self.force:
# logging.info('Deleting previous output directory')
# rm('-rf', self.outDir)
temp= self.dwi_file.split(',')
primaryVol= abspath(temp[0])
if len(temp)<2:
raise AttributeError('Two volumes are required for --imain')
else:
secondaryVol= abspath(temp[1])
primaryMask=[]
secondaryMask=[]
if self.b0_brain_mask:
temp = self.b0_brain_mask.split(',')
primaryMask = abspath(temp[0])
if len(temp) == 2:
secondaryMask = abspath(temp[1])
# obtain 4D/3D info and time axis info
dimension = load_nifti(primaryVol).header['dim']
dim1 = dimension[0]
if dim1!=4:
raise AttributeError('Primary volume must be 4D, however, secondary can be 3D/4D')
numVol1 = dimension[4]
dimension = load_nifti(secondaryVol).header['dim']
dim2 = dimension[0]
numVol2 = dimension[4]
temp= self.bvals_file.split(',')
if len(temp)>=1:
primaryBval= abspath(temp[0])
if len(temp)==2:
secondaryBval= abspath(temp[1])
elif len(temp)==1 and dim2==4:
secondaryBval= primaryBval
elif len(temp)==1 and dim2==3:
secondaryBval=[]
elif len(temp)==0:
raise AttributeError('--bvals are required')
temp= self.bvecs_file.split(',')
if len(temp)>=1:
primaryBvec= abspath(temp[0])
if len(temp)==2:
secondaryBvec= abspath(temp[1])
elif len(temp) == 1 and dim2 == 4:
secondaryBvec = primaryBvec
elif len(temp)==1 and dim2==3:
secondaryBvec=[]
else:
raise AttributeError('--bvecs are required')
with local.cwd(self.outDir):
# mask both volumes, fslmaths can do that irrespective of dimension
logging.info('Masking the volumes')
primaryMaskedVol = 'primary_masked.nii.gz'
secondaryMaskedVol = 'secondary_masked.nii.gz'
if primaryMask:
# mask the volume
fslmaths[primaryVol, '-mas', primaryMask, primaryMaskedVol] & FG
else:
primaryMaskedVol= primaryVol
if secondaryMask:
# mask the volume
fslmaths[secondaryVol, '-mas', secondaryMask, secondaryMaskedVol] & FG
else:
secondaryMaskedVol= secondaryVol
logging.info('Extracting B0 from masked volumes')
B0_PA= 'B0_PA.nii.gz'
B0_AP= 'B0_AP.nii.gz'
obtainB0(primaryMaskedVol, primaryBval, B0_PA, self.num_b0)
if dim2==4:
obtainB0(secondaryMaskedVol, secondaryBval, B0_AP, self.num_b0)
else:
B0_AP= secondaryMaskedVol
B0_PA_AP_merged = 'B0_PA_AP_merged.nii.gz'
with open(self.acqparams_file._path) as f:
acqp= f.read().strip().split('\n')
if len(acqp)!=2:
raise ValueError('The acquisition parameter file must have exactly two lines')
logging.info('Writing acqparams.txt for topup')
# firstDim: first acqp line should be replicated this number of times
firstB0dim= load_nifti(str(B0_PA)).header['dim'][4]
# secondDim: second acqp line should be replicated this number of times
secondB0dim= load_nifti(str(B0_AP)).header['dim'][4]
acqp_topup= 'acqp_topup.txt'
with open(acqp_topup,'w') as f:
for i in range(firstB0dim):
f.write(acqp[0]+'\n')
for i in range(secondB0dim):
f.write(acqp[1]+'\n')
logging.info('Merging B0_PA and BO_AP')
fslmerge('-t', B0_PA_AP_merged, B0_PA, B0_AP)
topup_params, applytopup_params, eddy_openmp_params= obtain_fsl_eddy_params(self.eddy_config_file._path)
# Example for topup
# === on merged b0 images ===
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#Running_topup_on_the_b.3D0_volumes
# topup --imain=P2A_A2P_b0 --datain=acqparams.txt --config=b02b0.cnf --out=my_output --iout=my_output
#
# === on all b0 images ===
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Running_topup
# topup --imain=all_b0s --datain=acqparams.txt --config=b02b0.cnf --out=my_output --iout=my_output
logging.info('Running topup')
topup_results= 'topup_out'
topupOut= 'topup_out.nii.gz'
# topup --iout yields as many volumes as there are input volumes
# --iout specifies the name of a 4D image file that contains unwarped and movement corrected images.
# each volume in the --imain will have a corresponding corrected volume in --iout.
# --iout is used for creating modified mask only
# when primary4D,secondary4D/3D are already masked, this will be useful
topup[f'--imain={B0_PA_AP_merged}',
f'--datain={acqp_topup}',
f'--out={topup_results}',
f'--iout={topupOut}',
topup_params.split()] & FG
# provide topupOutMean for quality checking
topupOutMean= 'topup_out_mean.nii.gz'
fslmaths[topupOut, '-Tmean', topupOutMean] & FG
logging.info('Running applytopup')
# applytopup always yields one output file regardless of one or two input files
# if two input files are provided, the resulting undistorted file will be a combination of the two
# containing only as many volumes as there are in one file
# B0_PA_correct, B0_AP_correct are for quality checking only
# primaryMaskCorrect, secondaryMaskCorrect will be associated masks
B0_PA_correct= 'B0_PA_corrected.nii.gz'
applytopup[f'--imain={B0_PA}',
f'--datain={self.acqparams_file}',
'--inindex=1',
f'--topup={topup_results}',
f'--out={B0_PA_correct}',
applytopup_params.split()] & FG
B0_AP_correct= 'B0_AP_corrected.nii.gz'
applytopup[f'--imain={B0_AP}',
f'--datain={self.acqparams_file}',
'--inindex=2',
f'--topup={topup_results}',
f'--out={B0_AP_correct}',
applytopup_params.split()] & FG
B0_PA_AP_corrected_merged= 'B0_PA_AP_corrected_merged'
fslmerge('-t', B0_PA_AP_corrected_merged, B0_PA_correct, B0_AP_correct)
fslmaths[B0_PA_AP_corrected_merged, '-Tmean', 'B0_PA_AP_corrected_mean'] & FG
topupMask= 'topup_mask.nii.gz'
# calculate topup mask
if primaryMask and secondaryMask:
fslmaths[primaryMask, '-mul', '1', primaryMask, '-odt', 'float']
fslmaths[secondaryMask, '-mul', '1', secondaryMask, '-odt', 'float']
applytopup_params+=' --interp=trilinear'
# this straightforward way could be used
'''
applytopup[f'--imain={primaryMask},{secondaryMask}',
f'--datain={self.acqparams_file}',
'--inindex=1,2',
f'--topup={topup_results}',
f'--out={topupMask}',
applytopup_params.split()] & FG
'''
# but let's do it step by step in order to have more control of the process
# binarise the mean of corrected primary,secondary mask to obtain modified mask
# use that mask for eddy_openmp
primaryMaskCorrect = 'primary_mask_corrected.nii.gz'
applytopup[f'--imain={primaryMask}',
f'--datain={self.acqparams_file}',
'--inindex=1',
f'--topup={topup_results}',
f'--out={primaryMaskCorrect}',
applytopup_params.split()] & FG
secondaryMaskCorrect = 'secondary_mask_corrected.nii.gz'
applytopup[f'--imain={secondaryMask}',
f'--datain={self.acqparams_file}',
'--inindex=2',
f'--topup={topup_results}',
f'--out={secondaryMaskCorrect}',
applytopup_params.split()] & FG
fslmerge('-t', topupMask, primaryMaskCorrect, secondaryMaskCorrect)
temp= load_nifti(topupMask)
data= temp.get_fdata()
data= abs(data[...,0])+ abs(data[...,1])
data[data!=0]= 1
# filter the mask to smooth edges
# scale num of erosion followed by scale num of dilation
# the greater the scale, the smoother the edges
# scale=2 seems sufficient
data= single_scale(data, int(self.scale))
save_nifti(topupMask, data.astype('uint8'), temp.affine, temp.header)
else:
# this block assumes the primary4D,secondary4D/3D are already masked
# then toupOutMean is also masked
# binarise the topupOutMean to obtain modified mask
# use that mask for eddy_openmp
# fslmaths[topupOutMean, '-bin', topupMask, '-odt', 'char'] & FG
# if --mask is not provided at all, this block creates a crude mask
# apply bet on the mean of topup output to obtain modified mask
# use that mask for eddy_openmp
bet[topupOutMean, topupMask.split('_mask.nii.gz')[0], '-m', '-n'] & FG
logging.info('Writing index.txt for topup')
indexFile= 'index.txt'
with open(indexFile, 'w') as f:
for i in range(numVol1):
f.write('1\n')
outPrefix = basename(primaryVol).split('.nii')[0]
# remove _acq-
outPrefix= outPrefix.replace('_acq-PA','')
outPrefix= outPrefix.replace('_acq-AP','')
# find dir field
if '_dir-' in primaryVol and '_dir-' in secondaryVol and self.whichVol == '1,2':
dir= load_nifti(primaryVol).shape[3]+ load_nifti(secondaryVol).shape[3]
outPrefix= local.path(re.sub('_dir-(.+?)_', f'_dir-{dir}_', outPrefix))
outPrefix = outPrefix + '_EdEp'
with open('.outPrefix.txt', 'w') as f:
f.write(outPrefix)
temp = self.whichVol.split(',')
if len(temp)==1 and temp[0]=='1':
# correct only primary4D volume
_eddy_openmp(primaryMaskedVol, primaryBval, primaryBvec, eddy_openmp_params)
elif len(temp)==2 and temp[1]=='2':
# sylvain would like to correct both primary and secondary volumes
with open(indexFile, 'a') as f:
for i in range(numVol2):
f.write('2\n')
# join both bvalFiles
bvals1= read_bvals(primaryBval)
if dim2==4 and not secondaryBval:
bvals2= bvals1.copy()
elif dim2==4 and secondaryBval:
bvals2= read_bvals(secondaryBval)
elif dim2==3:
bvals2=[0]
combinedBvals = 'combinedBvals.txt'
write_bvals(combinedBvals, bvals1+bvals2)
# join both bvecFiles
bvecs1= read_bvecs(primaryBvec)
if dim2==4 and not secondaryBvec:
bvecs2= bvecs1.copy()
elif dim2==4 and secondaryBvec:
bvecs2= read_bvecs(secondaryBvec)
elif dim2==3:
bvecs2=[[0,0,0]]
# join both bvecFiles
combinedBvecs = 'combinedBvecs.txt'
write_bvecs(combinedBvecs, bvecs1+bvecs2)
combinedData= 'combinedData.nii.gz'
fslmerge('-t', combinedData, primaryMaskedVol, secondaryMaskedVol)
_eddy_openmp(combinedData, combinedBvals, combinedBvecs, eddy_openmp_params)
else:
raise ValueError('Invalid --whichVol')
# rename topupMask to have same prefix as that of eddy corrected volume
move(topupMask, outPrefix + '_mask.nii.gz')