Exemple #1
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'registration',
                          'tensorfsl', 'hardidipy', 'tractquerier', 'qa')
     self.setCleanupBeforeImplement(False)
     self.absInDir = os.path.join(self.workingDir, 'input')
     self.relativeOutDir = 'output/subject/outlier_cleaned_tracts'
     self.absOutDir = os.path.join(self.workingDir, 'output')
Exemple #2
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 def __init__(self, subject):
     GenericTask.__init__(
             self, subject, 'upsampling', 'registration', 'masking', 'qa'
             )
     self.__dwiData = None
     self.__csdModel = None
     self.__csdPeaks = None
Exemple #3
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 def __init__(self, subject):
     GenericTask.__init__(
         self, subject, "preparation", "registration", "tensorfsl", "hardidipy", "tractquerier", "qa"
     )
     self.setCleanupBeforeImplement(False)
     self.relativeOutDir = "raw/outlier_cleaned_tracts"
     self.absOutDir = os.path.join(self.workingDir, "raw", "outlier_cleaned_tracts")
Exemple #4
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 def __init__(self, subject):
     GenericTask.__init__(self, subject,
                          'preparation', 'registration', 'tensorfsl',
                          'hardidipy', 'tractquerier', 'qa')
     self.setCleanupBeforeImplement(False)
     self.absInDir = os.path.join(self.workingDir, 'input')
     self.relativeOutDir = 'output/subject/outlier_cleaned_tracts'
     self.absOutDir = os.path.join(self.workingDir, 'output')
Exemple #5
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    def __init__(self, subject):
        GenericTask.__init__(
                self, subject, 'preparation', 'tensorfsl', 'tensormrtrix',
                'tensordipy', 'hardimrtrix', 'hardidipy', 'tractfiltering',)
        self.setCleanupBeforeImplement(False)

        self.absInDir = os.path.join(self.workingDir, 'input')
        self.absOutDir = os.path.join(self.workingDir, 'output')
 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'hardimrtrix',
             'masking', 'registration', 'atlasregistration' ,'qa')
     self.__tckDetRoiTrk = None
     self.__tckProbRoiTrk = None
     self.__tckgenRoiTrk = None
     self.__tcksiftRoiTrk = None
     self.__nbDirections = None
Exemple #7
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'hardimrtrix',
                          'masking', 'registration', 'atlasregistration',
                          'qa')
     self.__tckDetRoiTrk = None
     self.__tckProbRoiTrk = None
     self.__tckgenRoiTrk = None
     self.__tcksiftRoiTrk = None
     self.__nbDirections = None
Exemple #8
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    def __init__(self, subject):
        GenericTask.__init__(
            self,
            subject,
            'preparation',
            'tensorfsl',
            'tensormrtrix',
            'tensordipy',
            'hardimrtrix',
            'hardidipy',
            'tractfiltering',
        )
        self.setCleanupBeforeImplement(False)

        self.absInDir = os.path.join(self.workingDir, 'input')
        self.absOutDir = os.path.join(self.workingDir, 'output')
Exemple #9
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'parcellation', 'qa')
Exemple #10
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'registration', 'masking', 'qa')
     self.__fit = None
Exemple #11
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'parcellation', 'denoising', 'qa')
Exemple #12
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, "preparation", "correction", "denoising", "masking", "qa")
Exemple #13
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 def __init__(self, subject):
     GenericTask.__init__(
         self, subject,
         'preparation', 'upsampling', 'registration', 'atlasregistration',
         'tractographymrtrix', 'qa')
     self.setCleanupBeforeImplement(False)
Exemple #14
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 def __init__(self, subject):
     """Fits a diffusion tensor model at each voxel
     """
     GenericTask.__init__(self, subject, 'upsampling', 'registration',
                          'masking', 'qa')
Exemple #15
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'parcellation', 'qa')
Exemple #16
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'registration', 'tensormrtrix', 'tensordipy', 'tensorfsl',
          'hardidipy', 'hardimrtrix', 'tractographymrtrix', 'tractquerier', 'tractfiltering', 'tractometry')
     self.__finished = False
Exemple #17
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    def __init__(self, subject):

        GenericTask.__init__(self, subject, "masking", "registration",
                             "hardidipy")
Exemple #18
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'correction',
                          'denoising', 'masking', 'qa')
Exemple #19
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 def __init__(self, subject):
     self.subjectDir = subject.getDir()
     GenericTask.__init__(self, subject)
     self.setCleanupBeforeImplement(False)
Exemple #20
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, "upsampling", "registration", "masking", "qa")
     self.__dwiData = None
     self.__csdModel = None
     self.__csdPeaks = None
Exemple #21
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 def __init__(self, subject):
     GenericTask.__init__(self, subject,'preparation', 'parcellation', 'qa')
     self.matlabWarning = False
     self.sigmaVector = None
     self.algorithm = None
 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'atlas', 'upsampling', 'registration')
Exemple #23
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'backup', 'qa')
Exemple #24
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    def __init__(self, subject):
        """initialisation methods. Please leave as is"""

        GenericTask.__init__(self, subject, 'parcellation', 'qa')
Exemple #25
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 def __init__(self, subject):
     GenericTask.__init__(self, subject,'preparation', 'parcellation', 'qa')
     self.matlabWarning = False
     self.sigmaVector = None
     self.algorithm = None
Exemple #26
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'backup')
     self.setCleanupBeforeImplement(False)
     self.subjectName = subject.getName()
Exemple #27
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'backup')
     self.setCleanupBeforeImplement(False)
     self.subjectName = subject.getName()
Exemple #28
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'upsampling',
                          'registration', 'atlasregistration',
                          'tractographymrtrix', 'qa')
     self.setCleanupBeforeImplement(False)
    def __init__(self, subject):

        GenericTask.__init__(self, subject, "masking", "registration", "hardidipy")
Exemple #30
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'registration', 'tensormrtrix', 'tensordipy', 'tensorfsl', 'hardidipy', 'hardimrtrix')
     self.__finished = False
Exemple #31
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'correction', 'denoising', 'masking', 'qa')
Exemple #32
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'registration',
                          'tensormrtrix', 'tensordipy', 'tensorfsl',
                          'hardidipy', 'hardimrtrix', 'tractographymrtrix',
                          'tractquerier', 'tractfiltering', 'tractometry')
     self.__finished = False
Exemple #33
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'registration', 'upsampling', 'qa')
Exemple #34
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 def __init__(self, subject):
     self.subjectDir = subject.getDir()
     GenericTask.__init__(self, subject)
     self.setCleanupBeforeImplement(False)
Exemple #35
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'parcellation',
                          'denoising', 'qa')
Exemple #36
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'qa')
     self.id = self.get('id')
Exemple #37
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 def __init__(self, subject):
     """Fits a diffusion tensor model at each voxel
     """
     GenericTask.__init__(self, subject, 'upsampling', 'registration', 'masking', 'qa')
 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'hardimrtrix', 'masking', 'registration','qa')
Exemple #39
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'backup', 'qa')
Exemple #40
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    def __init__(self, subject):
        """initialisation methods. Please leave as is"""

        GenericTask.__init__(self, subject, 'parcellation', 'qa')
Exemple #41
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 def __init__(self, subject):
     GenericTask.__init__(
             self, subject, 'preparation', 'tensorfsl', 'tensormrtrix',
             'tensordipy', 'hardimrtrix', 'hardidipy', 'tractfiltering',)
     self.setCleanupBeforeImplement(False)
Exemple #42
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'parcellation', 'denoising', 'qa')
     self.__topupCorrection = False
     self.__fieldmapCorrection = False
Exemple #43
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'preparation', 'qa')
     self.id = self.get('id')
Exemple #44
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 def __init__(self, subject):
     GenericTask.__init__(self, subject, 'upsampling', 'registration',
                          'masking', 'qa')
     self.__dwiData = None
     self.__csdModel = None
     self.__csdPeaks = None