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LICENSE
MANIFEST.in
README.txt
setup.py
caps/__init__.py
caps/info.py
caps/toy_datasets.py
caps.egg-info/PKG-INFO
caps.egg-info/SOURCES.txt
caps.egg-info/dependency_links.txt
caps.egg-info/requires.txt
caps.egg-info/top_level.txt
caps/dicom_converter/__init__.py
caps/dicom_converter/dicom_deidentifier.py
caps/dicom_converter/dicom_deidentifier_v2.py
caps/dicom_converter/nifti_converter.py
caps/dicom_converter/base/__init__.py
caps/dicom_converter/base/csa2.py
caps/dicom_converter/base/split_series.py
caps/dicom_converter/base/tools.py
caps/diffusion_estimation/__init__.py
caps/diffusion_estimation/diffusion_multiprocessing.py
caps/diffusion_estimation/fsl_tensor_estimation.py
caps/diffusion_estimation/fvtk.py
caps/diffusion_estimation/integrals.py
caps/diffusion_estimation/monomials.py
caps/diffusion_estimation/polynomials.py
caps/diffusion_estimation/py_tensor_estimation.py
caps/diffusion_estimation/tensor_estimation.py
caps/diffusion_estimation/tensor_scalars.py
caps/diffusion_estimation/tensor_utils.py
caps/diffusion_estimation/resources/__init__.py
caps/diffusion_preproc/__init__.py
caps/diffusion_preproc/bet.py
caps/diffusion_preproc/eddy_correction.py
caps/diffusion_preproc/fsl_preproc.py
caps/diffusion_preproc/motion_correction.py
caps/diffusion_preproc/susceptibility_correction.py
caps/diffusion_registration/__init__.py
caps/diffusion_registration/fsl_registration.py
caps/diffusion_registration/reorientation.py
caps/functional_connectivity/__init__.py
caps/functional_connectivity/analysis.py
caps/functional_connectivity/conn.py
caps/functional_connectivity/manager.py
caps/functional_connectivity/matlab_utils.py
caps/functional_connectivity/results.py
caps/functional_connectivity/setup.py
caps/functional_connectivity/spatial_preproc.py
caps/functional_connectivity/temporal_preproc.py
caps/functional_connectivity/matlab_batch/__init__.py
caps/functional_preproc/__init__.py
caps/functional_preproc/pypreprocess_fmri_preproc.py
caps/preclinic_functional/__init__.py
caps/preclinic_functional/bet.py
caps/preclinic_functional/slice_timing.py
caps/preclinic_functional/spm_coregistration.py
caps/preclinic_functional/spm_new_segment.py
caps/preclinic_functional/spm_normalization.py
caps/preclinic_functional/spm_preproc.py
caps/preclinic_functional/spm_realignment.py
caps/preclinic_functional/spm_segment.py
caps/preclinic_functional/spm_smoothing.py
caps/preclinic_functional/spm_utility.py
caps/quality_assurance/__init__.py
caps/quality_assurance/fmri.py
caps/quality_control/__init__.py
caps/quality_control/brainvisa_map_cluster_analysis.py
caps/quality_control/fsl_interface.py
caps/quality_control/snapshots.py
caps/utils/__init__.py
caps/utils/bet.py
caps/utils/misc.py
doc/Makefile
doc/source/conf.py
doc/source/documentation.rst
doc/source/index.rst
doc/source/installation.rst
doc/source/_static/clustering.gif
doc/source/_static/nsap.png
doc/source/_static/nsap_full.png
doc/source/_static/technical_documentation/diffusion_estimation_ols.txt
doc/source/_static/technical_documentation/diffusion_estimation_quartics.txt
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doc/source/_static/technical_documentation/dt2_spectral_decomposition.txt
doc/source/_static/technical_documentation/dt4_scalars.txt
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doc/source/_templates/function.rst
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doc/source/_templates/nipype_class.rst
doc/source/_themes/scikit-learn/theme.conf
doc/source/_themes/scikit-learn/static/.Rhistory
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doc/source/generated/dicom_converter/index.rst
doc/source/generated/dicom_converter/pipeline/caps.dicom_converter.dicom_deidentifier.Dicom_anonymiser.rst
doc/source/generated/dicom_converter/pipeline/caps.dicom_converter.nifti_converter.Converter_nifti.rst
doc/source/generated/dicom_converter/pipeline/index.txt
doc/source/generated/dicom_converter/process/caps.dicom_converter.dicom_deidentifier.DeIdentifier.rst
doc/source/generated/dicom_converter/process/caps.dicom_converter.dicom_deidentifier.DicomWriter.rst
doc/source/generated/dicom_converter/process/caps.dicom_converter.dicom_deidentifier.InputDataManager.rst
doc/source/generated/dicom_converter/process/caps.dicom_converter.nifti_converter.InputDataManager.rst
doc/source/generated/dicom_converter/process/caps.dicom_converter.nifti_converter.NiftiHeaderFiller.rst
doc/source/generated/dicom_converter/process/index.txt
doc/source/generated/dicom_converter/schema/caps.dicom_converter.dicom_deidentifier.Dicom_anonymiser.png
doc/source/generated/dicom_converter/schema/caps.dicom_converter.nifti_converter.Converter_nifti.png
doc/source/generated/dicom_converter/use_cases/caps.dicom_converter.dicom_deidentifier.pilot.rst
doc/source/generated/dicom_converter/use_cases/caps.dicom_converter.nifti_converter.pilot.rst
doc/source/generated/dicom_converter/use_cases/index.txt
doc/source/generated/diffusion_estimation/index.rst
doc/source/generated/diffusion_estimation/pipeline/caps.diffusion_estimation.fsl_tensor_estimation.FSLTensorEstimation.rst
doc/source/generated/diffusion_estimation/pipeline/caps.diffusion_estimation.py_tensor_estimation.FourthOrderTensorEstimation.rst
doc/source/generated/diffusion_estimation/pipeline/caps.diffusion_estimation.py_tensor_estimation.SecondOrderTensorEstimation.rst
doc/source/generated/diffusion_estimation/pipeline/index.txt
doc/source/generated/diffusion_estimation/process/caps.diffusion_estimation.tensor_estimation.LSTensorEstimation.rst
doc/source/generated/diffusion_estimation/process/caps.diffusion_estimation.tensor_estimation.QUARTICTensorEstimation.rst
doc/source/generated/diffusion_estimation/process/caps.diffusion_estimation.tensor_scalars.FourthOrderScalarParameters.rst
doc/source/generated/diffusion_estimation/process/caps.diffusion_estimation.tensor_scalars.SecondOrderScalarParameters.rst
doc/source/generated/diffusion_estimation/process/caps.diffusion_estimation.tensor_utils.DecomposeSecondOrderTensor.rst
doc/source/generated/diffusion_estimation/process/index.txt
doc/source/generated/diffusion_estimation/schema/caps.diffusion_estimation.fsl_tensor_estimation.FSLTensorEstimation.png
doc/source/generated/diffusion_estimation/schema/caps.diffusion_estimation.py_tensor_estimation.FourthOrderTensorEstimation.png
doc/source/generated/diffusion_estimation/schema/caps.diffusion_estimation.py_tensor_estimation.SecondOrderTensorEstimation.png
doc/source/generated/diffusion_estimation/use_cases/caps.diffusion_estimation.fsl_tensor_estimation.pilot.rst
doc/source/generated/diffusion_estimation/use_cases/caps.diffusion_estimation.py_tensor_estimation.pilot_fourth_order.rst
doc/source/generated/diffusion_estimation/use_cases/caps.diffusion_estimation.py_tensor_estimation.pilot_second_order.rst
doc/source/generated/diffusion_estimation/use_cases/index.txt
doc/source/generated/diffusion_preproc/index.rst
doc/source/generated/diffusion_preproc/pipeline/caps.diffusion_preproc.bet.dBET.rst
doc/source/generated/diffusion_preproc/pipeline/caps.diffusion_preproc.fsl_preproc.FslDiffsuionPpreprocessings.rst
doc/source/generated/diffusion_preproc/pipeline/caps.diffusion_preproc.susceptibility_correction.SusceptibilityCorrection.rst
doc/source/generated/diffusion_preproc/pipeline/index.txt
doc/source/generated/diffusion_preproc/process/caps.diffusion_preproc.bet.ExtractReferenceB0Image.rst
doc/source/generated/diffusion_preproc/process/caps.diffusion_preproc.eddy_correction.EddyCorrection.rst
doc/source/generated/diffusion_preproc/process/caps.diffusion_preproc.motion_correction.TimeSerieMotionCorrection.rst
doc/source/generated/diffusion_preproc/process/index.txt
doc/source/generated/diffusion_preproc/schema/caps.diffusion_preproc.bet.dBET.png
doc/source/generated/diffusion_preproc/schema/caps.diffusion_preproc.fsl_preproc.FslDiffsuionPpreprocessings.png
doc/source/generated/diffusion_preproc/schema/caps.diffusion_preproc.susceptibility_correction.SusceptibilityCorrection.png
doc/source/generated/diffusion_preproc/use_cases/caps.diffusion_preproc.bet.pilot.rst
doc/source/generated/diffusion_preproc/use_cases/caps.diffusion_preproc.fsl_preproc.pilot.rst
doc/source/generated/diffusion_preproc/use_cases/index.txt
doc/source/generated/diffusion_registration/index.rst
doc/source/generated/diffusion_registration/pipeline/caps.diffusion_registration.fsl_registration.FSLRegistration.rst
doc/source/generated/diffusion_registration/pipeline/index.txt
doc/source/generated/diffusion_registration/process/caps.diffusion_registration.reorientation.LocalAffineTransformation.rst
doc/source/generated/diffusion_registration/process/caps.diffusion_registration.reorientation.SecondOrderTensorReorientation.rst
doc/source/generated/diffusion_registration/process/index.txt
doc/source/generated/diffusion_registration/schema/caps.diffusion_registration.fsl_registration.FSLRegistration.png
doc/source/generated/diffusion_registration/use_cases/caps.diffusion_registration.fsl_registration.pilot.rst
doc/source/generated/diffusion_registration/use_cases/index.txt
doc/source/generated/functional_connectivity/index.rst
doc/source/generated/functional_connectivity/pipeline/caps.functional_connectivity.conn.Conn.rst
doc/source/generated/functional_connectivity/pipeline/index.txt
doc/source/generated/functional_connectivity/process/caps.functional_connectivity.analysis.Analysis.rst
doc/source/generated/functional_connectivity/process/caps.functional_connectivity.manager.InputDataManager.rst
doc/source/generated/functional_connectivity/process/caps.functional_connectivity.results.Results.rst
doc/source/generated/functional_connectivity/process/caps.functional_connectivity.setup.Setup.rst
doc/source/generated/functional_connectivity/process/caps.functional_connectivity.spatial_preproc.SpatialPreproc.rst
doc/source/generated/functional_connectivity/process/caps.functional_connectivity.temporal_preproc.TemporalPreproc.rst
doc/source/generated/functional_connectivity/process/index.txt
doc/source/generated/functional_connectivity/schema/caps.functional_connectivity.conn.Conn.png
doc/source/generated/functional_connectivity/use_cases/caps.functional_connectivity.conn.pilot.rst
doc/source/generated/functional_connectivity/use_cases/index.txt
doc/source/generated/functional_preproc/index.rst
doc/source/generated/functional_preproc/pipeline/caps.functional_preproc.pypreprocess_fmri_preproc.SubjectPreprocessing.rst
doc/source/generated/functional_preproc/pipeline/index.txt
doc/source/generated/functional_preproc/process/caps.functional_preproc.pypreprocess_fmri_preproc.SPMSubjectPreprocessing.rst
doc/source/generated/functional_preproc/process/index.txt
doc/source/generated/functional_preproc/schema/caps.functional_preproc.pypreprocess_fmri_preproc.SubjectPreprocessing.png
doc/source/generated/functional_preproc/use_cases/caps.functional_preproc.pypreprocess_fmri_preproc.pilot.rst
doc/source/generated/functional_preproc/use_cases/index.txt
doc/source/generated/preclinic_functional/index.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.bet.BET.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.slice_timing.SliceTiming.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_coregistration.Coregistration.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_new_segment.SPMNewSegment.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_normalization.Normalization.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_preproc.SPMPreproc.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_realignment.Realignment.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_segment.SPMSegment.rst
doc/source/generated/preclinic_functional/pipeline/caps.preclinic_functional.spm_smoothing.Smoothing.rst
doc/source/generated/preclinic_functional/pipeline/index.txt
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.slice_timing.FSLSaveCustomTimings.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.slice_timing.InputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.slice_timing.OutputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_coregistration.InputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_coregistration.OutputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_new_segment.InputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_new_segment.ListDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_new_segment.OutputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_realignment.InputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_realignment.OutputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_segment.InputDataManager.rst
doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_segment.ListDataManager.rst
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doc/source/generated/preclinic_functional/process/caps.preclinic_functional.spm_smoothing.InputDataManager.rst
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doc/source/generated/preclinic_functional/process/index.txt
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.bet.BET.png
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.slice_timing.SliceTiming.png
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.spm_coregistration.Coregistration.png
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.spm_new_segment.SPMNewSegment.png
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.spm_normalization.Normalization.png
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.spm_preproc.SPMPreproc.png
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doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.spm_segment.SPMSegment.png
doc/source/generated/preclinic_functional/schema/caps.preclinic_functional.spm_smoothing.Smoothing.png
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.bet.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.slice_timing.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.spm_coregistration.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.spm_new_segment.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.spm_normalization.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.spm_preproc.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.spm_realignment.pilot.rst
doc/source/generated/preclinic_functional/use_cases/caps.preclinic_functional.spm_segment.pilot.rst
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doc/source/generated/quality_assurance/use_cases/caps.quality_assurance.fmri.pilot.rst
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doc/source/generated/quality_control/index.rst
doc/source/generated/quality_control/pipeline/caps.quality_control.brainvisa_map_cluster_analysis.MapClusterAnalysis.rst
doc/source/generated/quality_control/pipeline/caps.quality_control.snapshots.Snap.rst
doc/source/generated/quality_control/pipeline/index.txt
doc/source/generated/quality_control/process/caps.quality_control.brainvisa_map_cluster_analysis.MapToMesh.rst
doc/source/generated/quality_control/process/caps.quality_control.brainvisa_map_cluster_analysis.MeshClusterRendering.rst
doc/source/generated/quality_control/process/caps.quality_control.snapshots.MultiSnapshot.rst
doc/source/generated/quality_control/process/caps.quality_control.snapshots.SnapView.rst
doc/source/generated/quality_control/process/index.txt
doc/source/generated/quality_control/schema/caps.quality_control.brainvisa_map_cluster_analysis.MapClusterAnalysis.png
doc/source/generated/quality_control/schema/caps.quality_control.snapshots.Snap.png
doc/source/generated/quality_control/use_cases/caps.quality_control.brainvisa_map_cluster_analysis.pilot.rst
doc/source/generated/quality_control/use_cases/caps.quality_control.snapshots.pilot.rst
doc/source/generated/quality_control/use_cases/index.txt
doc/source/generated/utils/index.rst
doc/source/generated/utils/pipeline/caps.utils.bet.BET.rst
doc/source/generated/utils/pipeline/caps.utils.misc.ApplyXfm.rst
doc/source/generated/utils/pipeline/index.txt
doc/source/generated/utils/process/caps.utils.misc.Select.rst
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doc/source/generated/utils/use_cases/caps.utils.bet.pilot.rst
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