DTI_Register ============ Register DTI to the fixed volume using DTIReg :Command: ``dmriprep`` :Module version: 0.1 :Module type: ``prep`` :Attributes: ``utility``, ``indentity`` :Notes: `DTI_Register README `_ :Source: `dtiplayground/dmri/preprocessing/modules/DTI_Register `_ Global variables ---------------- Values this module shares with the other modules of the pipeline (``dmriprep run -g =`` sets one). - ``dti_path`` - ``displacement_field_path`` - ``inverse_displacement_field_path`` - ``registered_dti_path`` - ``initial_affine_path`` - ``registered_metric_paths`` - ``reference_dti_path`` - ``tensor_flip_applied`` Command line variables ---------------------- Values this module shares with the other modules of the pipeline (``dmriprep run -g =`` sets one). - ``reference_dti`` - ``reference_normative_model`` - ``age`` - ``tensor_flip`` Protocol options ---------------- ``method`` Method to register DTI (ANTs) :Type: ``list`` :Default: ``ANTs`` :Choices: - ``ANTs`` -- Use ANTs to register ``referenceImage`` Reference (Fixed Image) :Type: ``string`` :Default: not set ``referenceNormativeModel`` Normative model of the reference atlas (folder with manifest.json and /DTI\_mean.nrrd, written by 'dmrifiberprofile qc-registration --build-normative'). The DTI is then registered to the mean tensor of the age bin of the subject instead of the reference image; without an age, or a matching bin, the reference image is used :Type: ``dirpath-remote`` :Default: not set ``age`` Age of the subject in the unit of the age bins of the normative model (months); taken from ageCSV, or read from the image path with ageRegex, if not set :Type: ``float`` :Default: not set ``ageCSV`` CSV/TSV with the age of each scan (as 'dmrifiberprofile qc-registration --age-csv'), for cohorts whose session names don't carry the age. Subject and session columns are detected (participant\_id/session\_id and variants); one row per subject applies to all of its sessions. The subject and session of the scan are read from its path (sub-, ses-) :Type: ``filepath-remote`` :Default: not set ``ageColumn`` Name of the ageCSV column holding the age (default - auto-detect - age, age\_months, candidate\_age, ...) :Type: ``string`` :Default: not set ``ageUnits`` Units of the age column of ageCSV (converted to the months of the age bins) :Type: ``list`` :Default: ``months`` :Choices: - ``months`` -- Ages of ageCSV are in months - ``years`` -- Ages of ageCSV are in years - ``weeks`` -- Ages of ageCSV are in weeks - ``days`` -- Ages of ageCSV are in days ``ageRegex`` Regular expression for the age in the path of the input image (group 1), used when neither age nor ageCSV gives one :Type: ``string`` :Default: ``ses-(\d+)m`` ``ANTsPath`` ANTs installation directory (default is dtiplayground-tools/ANTs) :Type: ``dirpath-remote`` :Default: ``$ANTSDIR`` ``ANTsMethod`` ANTS method :Type: ``string`` :Default: ``useScalar-ANTS`` ``registrationType`` Registration Type :Type: ``list`` :Default: ``GreedyDiffeo`` :Choices: - ``GreedyDiffeo`` -- Greedy Diffeo ``similarityMetric`` Similarity Metric :Type: ``list`` :Default: ``CC`` :Choices: - ``CC`` -- Cross Correlation ``similarityParameter`` Similarity Parameter (radius of the CC metric) :Type: ``number`` :Default: ``2`` ``ANTsIterations`` Iteration parameter for ANTS :Type: ``string`` :Default: ``100x50x20`` ``gaussianSigma`` Gaussian Sigma :Type: ``number`` :Default: ``1`` ``ANTsTransformationStep`` Gradient step of the ANTS transformation :Type: ``number`` :Default: ``0.25`` ``ANTsUseHistogramMatching`` Match the histograms of the scalar images before the ANTS registration :Type: ``boolean`` :Default: ``true`` ``scalarMeasurement`` Scalar image of the tensors used for the registration (DTI-Reg and BRAINSFit) :Type: ``list`` :Default: ``FA`` :Choices: - ``FA`` -- Register the FA images of the tensors - ``MD`` -- Register the MD images of the tensors ``tensorCorrection`` Correction of tensors with negative eigenvalues when computing the scalar images and resampling :Type: ``list`` :Default: ``abs`` :Choices: - ``abs`` -- Negative eigenvalues are replaced by their absolute value - ``zero`` -- Negative eigenvalues are set to zero - ``nearest`` -- Nearest positive definite tensor - ``none`` -- No correction ``initialAffine`` Initial affine transform of the DTI to the reference, refined by the ANTS registration :Type: ``list`` :Default: ``BRAINSFit`` :Choices: - ``BRAINSFit`` -- Affine registration of the scalar images with BRAINSFit (fixed = reference, moving = DTI) - ``file`` -- Use the transform given in initialAffineFile - ``none`` -- No initial affine transform ``initialAffineFile`` ITK transform file (fixed = reference, moving = DTI), used if initialAffine is 'file' :Type: ``string`` :Default: not set ``tensorFlip`` Flip of the tensor frame applied to the DTI before the registration: none (also if empty and the global variable tensor\_flip isn't set), auto (detected: agreement of the principal directions with the reference after the initial affine, or their coherence along the tracts without an initial affine), the axes to flip (e.g. x or x,z), or voxel for components in the frame of the voxel axes (rotated into the space of the header; with flips e.g. voxel,x) :Type: ``string`` :Default: not set ``tensorFlipFAThreshold`` FA threshold of the white matter voxels used by the automatic flip detection :Type: ``number`` :Default: ``0.3`` ``BRAINSFitTransforms`` Comma delimited BRAINSFit transform stages (Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine), run in this order :Type: ``string`` :Default: ``Rigid,Affine`` ``BRAINSFitInitializeTransformMode`` Initialization of the BRAINSFit registration :Type: ``list`` :Default: ``useCenterOfHeadAlign`` :Choices: - ``useCenterOfHeadAlign`` -- Align the centers of the heads - ``useMomentsAlign`` -- Align the centers of mass and principal axes - ``useGeometryAlign`` -- Align the image centers - ``Off`` -- No initialization ``BRAINSFitSamplingPercentage`` Fraction (0-1) of the voxels sampled for the BRAINSFit metric. Default 0.5; smaller values are faster but less reproducible (BRAINSFit default 0.002 gave initial affines several mm apart between repeated runs) :Type: ``number`` :Default: ``0.5`` ``registerMetrics`` Apply the displacement field to the diffusion metrics in the folder of the input DTI that share its file name prefix (e.g. \_dwi\_QCed\_FA.nii.gz for \_dwi\_QCed\_tensor.nrrd). Tensor images (e.g. free-water corrected tensors) are resampled log-Euclidean with reorientation like the DTI, scalar images linearly. Written as registered\_ :Type: ``boolean`` :Default: ``true`` ``metricExclude`` Comma delimited parts of file names that are not registered (e.g. brain masks); integer images and images that are neither scalar nor tensor are not registered either :Type: ``string`` :Default: ``mask``