def eddyCorrection(self,filename, ref=0):
from PythonDiffusion import eddyCorrection
starttime=datetime.now()
print "Applying eddy current correction."
eddyCorrection(self, filename, ref)
time=datetime.now()-starttime
print "Eddy current correction completed in %r seconds." %time.seconds
def eddyCorrection(self, filename=0, ref=0, protocol='eddy_v'):
from PythonDiffusion import eddyCorrection
starttime = datetime.now()
print "Applying eddy current correction."
if filename == 0:
filename = self.name + '_EC'
eddyCorrection(self, filename=filename, ref=ref, protocol=protocol)
time = datetime.now() - starttime
print "Eddy current correction completed in %r seconds." % time.seconds
def processDiffusion(self,ec=False, bv=None):
print "Processing diffusion, full pipeline."
from PythonDiffusion import rescaleImage, eddyCorrection
from datetime import datetime
if self.nrep==1:
print "Applying slope correction..."
rescaleImage(self)
if ec:
print "ec=True. Applying eddy current correction."
eddyCorrection(self,self.name+'_EC', protocol='eddy_v')
self.tensorFit(bv=bv)
def processDiffusion(self,
ec=False,
bv=None,
mode='dti',
removea0=0,
mask=True):
print "Processing diffusion, full pipeline."
from PythonDiffusion import rescaleImage, eddyCorrection
from datetime import datetime
if self.nrep == 1:
print "Applying slope correction..."
rescaleImage(self)
if ec:
print "ec=True. Applying eddy current correction."
eddyCorrection(self, self.name + '_EC', protocol='eddy_correct')
if mode == 'dti' or mode == 'RESTORE':
self.tensorFit(bv=bv, removea0=removea0, m=mode, mask=mask)
elif mode == 'dki':
self.processKurtosis()
os.path.join(filen, filen + "_nonselT1fit"))
aslimg.save_output(os.path.join(filen, filen + '_Full'))
pl.close()
except ValueError:
print "Image shape incorrect: ", aslimg.shape, "Not compatible with amount of inversion times provided."
elif ("dti" in im.protocol.lower() or "dwi" in im.protocol.lower()
or "dki" in im.protocol.lower()
or 'trace' in im.protocol.lower()) and im.name[-1] == '1':
dtimg = DiffusionImg(filen)
if not ((len(dtimg.bvals) - dtimg.nA0) / len(dtimg.dwdir) >= 1
and len(dtimg.dwdir) > 5):
if EC:
from PythonDiffusion import eddyCorrection
eddyCorrection(dtimg,
dtimg.name + '_EC',
protocol='eddy_correct')
if (len(dtimg.bvals) - dtimg.nA0) / len(dtimg.dwdir) == 1:
print "Single b-value found, but not enough directions to fit a tensor. Calculating trace image."
dtimg.trace_1b()
nif = nib.Nifti1Image(dtimg.trace, dtimg.affine)
nib.save(nif, filen + '_trace.nii')
elif (len(dtimg.bvals) - dtimg.nA0) / len(dtimg.dwdir) > 1:
print "Multiple b-values found, but not enough directions to fit a tensor. Fitting trace image."
dtimg.trace_multib()
nif = nib.Nifti1Image(dtimg.trace, dtimg.affine)
nib.save(nif, filen + '_trace.nii')
elif os.path.isfile(dtimg.name +
'_EC.nii.gz') or os.path.isfile(dtimg.name +
'_EC.nii'):