def __convertDwi(self, sequence, session, target):
""" Convert a dwi dicom images into nifti
the name of the resulting image will be:
prefix_subjectName.nii.gz
"""
dwi = util.buildName(self.__configParser, target, sequence.getPrefix().getValue(), session.getName(),'nii.gz')
bEnc = util.buildName(self.__configParser, target, dwi, None, "b")
bvals = util.buildName(self.__configParser, target, dwi, None, "bvals")
bvecs = util.buildName(self.__configParser, target, dwi, None, "bvecs")
cmd = "mrconvert {} {} -force -export_grad_mrtrix {} -export_grad_fsl {} {}"\
.format(sequence.getEscapedDirectory(), dwi, bEnc, bvecs, bvals)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3,4 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig( self.__configFilename)
util.launchCommand(cmd)
def __convertDwi(self, sequence, session, target):
""" Convert a dwi dicomparser images into nifti
the name of the resulting image will be:
prefix_subjectName.nii.gz
"""
dwi = util.buildName(self.__configParser, target,
sequence.getPrefix().getValue(),
session.getName(), 'nii.gz')
bEnc = util.buildName(self.__configParser, target, dwi, None, "b")
bvals = util.buildName(self.__configParser, target, dwi, None, "bvals")
bvecs = util.buildName(self.__configParser, target, dwi, None, "bvecs")
cmd = "mrconvert {} {} -force -export_grad_mrtrix {} -export_grad_fsl {} {}"\
.format(sequence.getEscapedDirectory(), dwi, bEnc, bvecs, bvals)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3,4 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig(self.__configFilename)
def __convert(self, sequence, session, target):
filename = util.buildName(self.__configParser, target, sequence.getPrefix().getValue(), session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
if sequence.getPrefix().getName() == 'phase':
cmd += " -datatype float32 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig(self.__configFilename)
def __convert(self, sequence, session, target):
filename = util.buildName(self.__configParser, target,
sequence.getPrefix().getValue(),
session.getName(), 'nii.gz')
cmd = "mrconvert {0} {1} -force ".format(
sequence.getEscapedDirectory(), filename)
if not self.__arguments.noStride:
cmd += " -stride 1,2,3 "
if sequence.getPrefix().getName() == 'phase':
cmd += " -datatype float32 "
print cmd
util.launchCommand(cmd)
if not self.__arguments.noConfig:
dicoms = glob.glob("{}/*.dcm".format(sequence.getDirectory()))
if len(dicoms) > 0:
toadinfo = Toadinfo(dicoms.pop())
toadinfo.writeToadConfig(self.__configFilename)