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"motivation"], [21, "motivation"], [29, "motivation"]], "Overview": [[10, "overview"], [11, "overview"], [18, "overview"], [44, "overview"], [45, "overview"], [49, "overview"], [54, "overview"], [55, "overview"]], "Issues": [[10, "issues"], [11, "issues"], [21, "issues"]], "DcmMetaExtension tied to NiftiExtension": [[10, "dcmmetaextension-tied-to-niftiextension"]], "Plan": [[10, "plan"], [10, "id1"], [10, "id2"], [10, "id3"]], "Keeping track of metadata when manipulating images": [[10, "keeping-track-of-metadata-when-manipulating-images"]], "Detecting slice or volume-specific data difficult for 3D and 4D DICOMS": [[10, "detecting-slice-or-volume-specific-data-difficult-for-3d-and-4d-dicoms"]], "Meta data in nested DICOM sequences can not be independently classified": [[10, "meta-data-in-nested-dicom-sequences-can-not-be-independently-classified"]], "Improving access to varying meta data through the Nifti": [[10, "improving-access-to-varying-meta-data-through-the-nifti"]], "BIAP5 - A streamlines converter": [[11, "biap5-a-streamlines-converter"]], "Header": [[11, "header"]], "Future Work": [[11, "future-work"]], "BIAP6 - Identifying image axes": [[12, "biap6-identifying-image-axes"]], "Time axis as the fourth axis": [[12, "time-axis-as-the-fourth-axis"]], "Images can have more than four axes": [[12, "images-can-have-more-than-four-axes"]], "The current nibabel convention": [[12, "the-current-nibabel-convention"]], "Distinguishing time and volume": [[12, "distinguishing-time-and-volume"]], "Possible solutions to finding axes": [[12, "possible-solutions-to-finding-axes"]], "General solution: associating axes and labels": [[12, "general-solution-associating-axes-and-labels"]], "Using convention : enforcing time as 4th axis": [[12, "using-convention-enforcing-time-as-4th-axis"]], "BIAP7 - Loading multiple images": [[13, "biap7-loading-multiple-images"]], "Some formats store images with different shapes in the same file": [[13, "some-formats-store-images-with-different-shapes-in-the-same-file"]], "It can be useful to load 4D images as multiple 3D images": [[13, "it-can-be-useful-to-load-4d-images-as-multiple-3d-images"]], "Options": [[13, "options"]], "Return an image sequence from load for some file formats": [[13, "return-an-image-sequence-from-load-for-some-file-formats"]], "Add a load_multi top-level function": [[13, "add-a-load-multi-top-level-function"]], "Next steps:": [[13, "next-steps"]], "BIAP8 - Always load image data as floating point": [[14, "biap8-always-load-image-data-as-floating-point"]], "Summary": [[14, "summary"], [21, "summary"], [29, "summary"]], "In detail": [[14, "in-detail"], [44, "in-detail"], [49, "in-detail"], [54, "in-detail"], [55, "in-detail"]], "Current implementation": [[14, "current-implementation"], [20, "current-implementation"]], "Proposal - add, prefer get_fdata method": [[14, "proposal-add-prefer-get-fdata-method"]], "BIAP9 - The Coordinate Image API": [[15, "biap9-the-coordinate-image-api"]], "Surface data is generally kept separate from geometric metadata": [[15, "surface-data-is-generally-kept-separate-from-geometric-metadata"]], "Terminology": [[15, "terminology"]], "Currently supported surface formats": [[15, "currently-supported-surface-formats"]], "Other relevant formats": [[15, "other-relevant-formats"]], "Desiderata for an API supporting surfaces": [[15, "desiderata-for-an-api-supporting-surfaces"]], "Prominent use cases": [[15, "prominent-use-cases"]], "Modeling": [[15, "modeling"]], "Smoothing": [[15, "smoothing"]], "Plotting": [[15, "plotting"]], "Subsampling CIFTI-2": [[15, "subsampling-cifti-2"]], "BIAP X \u2014 Template and Instructions": [[16, "biap-x-template-and-instructions"]], "Motivation and Scope": [[16, "motivation-and-scope"]], "Usage and Impact": [[16, "usage-and-impact"]], "Backward compatibility": [[16, "backward-compatibility"]], "Detailed description": [[16, "detailed-description"]], "Related Work": [[16, "related-work"]], "Discussion": [[16, "discussion"]], "BIAPs": [[17, "biaps"]], "BrainVoyager file formats": [[18, "brainvoyager-file-formats"]], "BV internal format axes": [[18, "bv-internal-format-axes"]], "Types of BV files": [[18, "types-of-bv-files"]], "Core Developer Guide": [[19, "core-developer-guide"]], "Reviewing": [[19, "reviewing"]], "How to Conduct A Good Review": [[19, "how-to-conduct-a-good-review"]], "Merge Only Changes You Understand": [[19, "merge-only-changes-you-understand"]], "Closing issues and pull requests": [[19, "closing-issues-and-pull-requests"]], "Further resources": [[19, "further-resources"]], "Acknowledgments": [[19, "acknowledgments"], [25, "acknowledgments"]], "Design of data packages for the nibabel and the nipy suite": [[20, "design-of-data-packages-for-the-nibabel-and-the-nipy-suite"]], "Use cases for data packages": [[20, "use-cases-for-data-packages"]], "Using the data package": [[20, "using-the-data-package"]], "Warnings during installation": [[20, "warnings-during-installation"]], "Finding the data": [[20, "finding-the-data"]], "Requirements for a data package": [[20, "requirements-for-a-data-package"]], "Data package format": [[20, "data-package-format"]], "Installing the data": [[20, "installing-the-data"]], "Packaging for distributions": [[20, "packaging-for-distributions"]], "Principles of data package": [[21, "principles-of-data-package"]], "Separation of ideas": [[21, "separation-of-ideas"]], "Package": [[21, "package"]], "Package name": [[21, "package-name"]], "Package instantiation": [[21, "package-instantiation"]], "Pinstance revision": [[21, "pinstance-revision"]], "Pinstance revision id": [[21, "pinstance-revision-id"]], "Pinstance tag": [[21, "pinstance-tag"]], "Pinstance version": [[21, "pinstance-version"]], "Package provider bundle": [[21, "package-provider-bundle"]], "Provider bundle format": [[21, "provider-bundle-format"]], "Pinstance release": [[21, "pinstance-release"]], "Prundle discovery": [[21, "prundle-discovery"]], "Prundle discovery source": [[21, "prundle-discovery-source"]], "Pinstance metadata query": [[21, "pinstance-metadata-query"]], "Pinstance metadata query source": [[21, "pinstance-metadata-query-source"]], "Pinstance installation": [[21, "pinstance-installation"]], "Data and metadata": [[21, "data-and-metadata"]], "Comparative terminology": [[21, "comparative-terminology"]], "Compared to Debian packaging": [[21, "compared-to-debian-packaging"]], "Desiderata": [[21, "desiderata"]], "Dependency management": [[21, "dependency-management"]], "Authentication and validation": [[21, "authentication-and-validation"]], "Differences from code packages": [[21, "differences-from-code-packages"]], "Some usecases": [[21, "some-usecases"]], "Discovery": [[21, "discovery"], [22, "discovery"]], "Data package usecases and implementation": [[22, "data-package-usecases-and-implementation"]], "Usecases": [[22, "usecases"]], "Prundles": [[22, "prundles"]], "Examples": [[22, "examples"], [79, "examples"]], "Create local-path prundle": [[22, "create-local-path-prundle"]], "Getting prundle data": [[22, "getting-prundle-data"]], "Discovery sources": [[22, "discovery-sources"], [22, "id1"]], "Default discovery sources": [[22, "default-discovery-sources"]], "Discovery source pools": [[22, "discovery-source-pools"]], "Register a prundle": [[22, "register-a-prundle"]], "Local path prundles": [[22, "local-path-prundles"]], "Registering a package": [[22, "registering-a-package"]], "Using discovery sources without dpkg": [[22, "using-discovery-sources-without-dpkg"]], "Developer discussions": [[23, "developer-discussions"]], "NiBabel Developer Guidelines": [[24, "nibabel-developer-guidelines"]], "NiBabel source code": [[24, "nibabel-source-code"]], "Documentation": [[24, "documentation"], [58, "id1"]], "Code Documentation": [[24, "code-documentation"]], "Git Repository": [[24, "git-repository"]], "Layout": [[24, "layout"]], "Commits": [[24, "commits"]], "Merges": [[24, "merges"]], "Changelog": [[24, "changelog"]], "Community guidelines": [[24, "code-of-conduct"]], "Governance and Decision Making": [[25, "governance-and-decision-making"]], "Roles And Responsibilities": [[25, "roles-and-responsibilities"]], "The Community": [[25, "the-community"]], "Contributors": [[25, "contributors"]], "Core Developers": [[25, "core-developers"]], "Steering Council": [[25, "steering-council"]], "Decision Making Process": [[25, "decision-making-process"]], "Enhancement Proposals (BIAPs)": [[25, "enhancement-proposals-biaps"]], "The nibabel image object": [[26, "the-nibabel-image-object"]], "Developer documentation page": [[27, "developer-documentation-page"]], "A guide to making a nibabel release": [[28, "a-guide-to-making-a-nibabel-release"]], "Release checklist": [[28, "release-checklist"]], "Keeping track of whether images have been modified since load": [[29, "keeping-track-of-whether-images-have-been-modified-since-load"]], "Possible implementation": [[29, "possible-implementation"]], "Roadmap": [[30, "roadmap"]], "Expressive API": [[30, "expressive-api"]], "Axis and tick labels": [[30, "axis-and-tick-labels"]], "API for surface data": [[30, "api-for-surface-data"]], "Range": [[30, "range"]], "Spatial transforms": [[30, "spatial-transforms"]], "Scalefactors and intercepts": [[31, "scalefactors-and-intercepts"]], "Image use-cases in SPM": [[32, "image-use-cases-in-spm"]], "SPM image methods / functions": [[32, "spm-image-methods-functions"]], "dcm2nii algorithms": [[33, "dcm2nii-algorithms"]], "Compiling dcm2nii": [[33, "compiling-dcm2nii"]], "Some tag modifications": [[33, "some-tag-modifications"]], "Sorting slices into volumes": [[33, "sorting-slices-into-volumes"]], "DICOM concepts and implementations": [[34, "dicom-concepts-and-implementations"]], "DICOM fields": [[35, "dicom-fields"]], "Fields for ordering DICOM files into images": [[35, "fields-for-ordering-dicom-files-into-images"]], "Multi-frame images": [[35, "multi-frame-images"]], "DICOM information": [[36, "dicom-information"]], "Sample images": [[36, "sample-images"]], "Introduction to DICOM": [[37, "introduction-to-dicom"]], "DICOM is messages": [[37, "dicom-is-messages"]], "The DICOM standard": [[37, "the-dicom-standard"]], "DICOM data format": [[37, "dicom-data-format"]], "DICOM elements": [[37, "dicom-elements"]], "Attribute Tag": [[37, "attribute-tag"]], "Standard attribute tags": [[37, "standard-attribute-tags"]], "Private attribute tags": [[37, "private-attribute-tags"]], "Value Representation": [[37, "value-representation"]], "Value length": [[37, "value-length"]], "Value field": [[37, "value-field"]], "Data element tags and data dictionaries": [[37, "data-element-tags-and-data-dictionaries"]], "Value Representation in the data dictionary": [[37, "value-representation-in-the-data-dictionary"]], "Value Multiplicity in the data dictionary": [[37, "value-multiplicity-in-the-data-dictionary"]], "DICOM data structures": [[37, "dicom-data-structures"]], "A data set": [[37, "a-data-set"]], "Background - the DICOM world": [[37, "background-the-dicom-world"]], "DICOM Entities and Information Object Definitions": [[37, "dicom-entities-and-information-object-definitions"]], "DICOM services (DIMSE)": [[37, "dicom-services-dimse"]], "DICOM service object pairs (SOPs)": [[37, "dicom-service-object-pairs-sops"]], "DICOM files": [[37, "dicom-files"]], "Siemens mosaic format": [[38, "siemens-mosaic-format"]], "Getting the slices from the mosaic": [[38, "getting-the-slices-from-the-mosaic"]], "DICOM orientation for mosaic": [[38, "dicom-orientation-for-mosaic"]], "Data scaling": [[38, "data-scaling"], [65, "data-scaling"]], "DICOM Tags in the NIfTI Header": [[39, "dicom-tags-in-the-nifti-header"]], "Defining the DICOM orientation": [[40, "defining-the-dicom-orientation"]], "DICOM patient coordinate system": [[40, "dicom-patient-coordinate-system"]], "DICOM pixel data": [[40, "dicom-pixel-data"]], "Pixel spacing": [[40, "pixel-spacing"]], "DICOM voxel to patient coordinate system mapping": [[40, "dicom-voxel-to-patient-coordinate-system-mapping"]], "(i, j), columns, rows in DICOM": [[40, "i-j-columns-rows-in-dicom"]], "DICOM affines again": [[40, "dicom-affines-again"]], "DICOM affine formula": [[40, "dicom-affine-formula"]], "Getting a 3D affine from a DICOM slice or list of slices": [[40, "getting-a-3d-affine-from-a-dicom-slice-or-list-of-slices"]], "DICOM affine Definitions": [[40, "dicom-affine-definitions"]], "Derivations": [[40, "derivations"]], "3D affine formulae": [[40, "d-affine-formulae"]], "Working out the Z coordinates for a set of slices": [[40, "working-out-the-z-coordinates-for-a-set-of-slices"]], "Siemens format DICOM with CSA header": [[41, "siemens-format-dicom-with-csa-header"]], "CSA header": [[41, "csa-header"]], "CSA1": [[41, "csa1"]], "Start header": [[41, "start-header"], [41, "id2"]], "Each tag": [[41, "each-tag"], [41, "id3"]], "Each item": [[41, "each-item"], [41, "id4"]], "CSA2": [[41, "csa2"]], "SPM DICOM conversion": [[42, "spm-dicom-conversion"]], "spm_dicom_dict.mat": [[42, "spm-dicom-dict-mat"]], "spm_dicom_headers.m": [[42, "spm-dicom-headers-m"]], "File opening": [[42, "file-opening"]], "tag read for Philips Integra": [[42, "tag-read-for-philips-integra"]], "Tag length": [[42, "tag-length"]], "SQ VR type (Sequence of items type)": [[42, "sq-vr-type-sequence-of-items-type"]], "spm_dicom_convert.m": [[42, "spm-dicom-convert-m"]], "File categorization": [[42, "file-categorization"]], "Sorting files into volumes": [[42, "sorting-files-into-volumes"]], "First pass": [[42, "first-pass"]], "Second pass": [[42, "second-pass"]], "Final check": [[42, "final-check"]], "Possible volume resort": [[42, "possible-volume-resort"]], "Writing DICOM volumes": [[42, "writing-dicom-volumes"]], "Making the affine": [[42, "making-the-affine"]], "Writing the voxel data": [[42, "writing-the-voxel-data"]], "Getting Started": [[43, "getting-started"]], "Configure git": [[44, "configure-git"]], "user.name and user.email": [[44, "user-name-and-user-email"]], "Aliases": [[44, "aliases"]], "Editor": [[44, "editor"]], "Merging": [[44, "merging"]], "Fancy log output": [[44, "fancy-log-output"]], "Development workflow": [[45, "development-workflow"]], "Workflow summary": [[45, "workflow-summary"]], "Consider deleting your master branch": [[45, "consider-deleting-your-master-branch"]], "Update the mirror of trunk": [[45, "update-the-mirror-of-trunk"]], "Make a new feature branch": [[45, "make-a-new-feature-branch"]], "The editing workflow": [[45, "the-editing-workflow"]], "In more detail": [[45, "in-more-detail"]], "Ask for your changes to be reviewed or merged": [[45, "ask-for-your-changes-to-be-reviewed-or-merged"]], "Some other things you might want to do": [[45, "some-other-things-you-might-want-to-do"]], "Delete a branch on github": [[45, "delete-a-branch-on-github"]], "Several people sharing a single repository": [[45, "several-people-sharing-a-single-repository"]], "Explore your repository": [[45, "explore-your-repository"]], "Rebasing on trunk": [[45, "rebasing-on-trunk"]], "Recovering from mess-ups": [[45, "recovering-from-mess-ups"]], "Rewriting commit history": [[45, "rewriting-commit-history"]], "Following the latest source": [[46, "following-the-latest-source"]], "Get the local copy of the code": [[46, "get-the-local-copy-of-the-code"]], "Updating the code": [[46, "updating-the-code"]], "Making your own copy (fork) of nibabel": [[47, "making-your-own-copy-fork-of-nibabel"]], "Set up and configure a github account": [[47, "set-up-and-configure-a-github-account"]], "Create your own forked copy of nibabel": [[47, "create-your-own-forked-copy-of-nibabel"]], "Git for development": [[48, "git-for-development"]], "Install git": [[49, "install-git"]], "Introduction": [[50, "introduction"]], "git resources": [[51, "git-resources"]], "Tutorials and summaries": [[51, "tutorials-and-summaries"]], "Advanced git workflow": [[51, "advanced-git-workflow"]], "Manual pages online": [[51, "manual-pages-online"]], "Working with nibabel source code": [[52, "working-with-nibabel-source-code"]], "Maintainer workflow": [[53, "maintainer-workflow"]], "Integrating changes": [[53, "integrating-changes"]], "A few commits": [[53, "a-few-commits"]], "A long series of commits": [[53, "a-long-series-of-commits"]], "Check the history": [[53, "check-the-history"]], "Push to trunk": [[53, "push-to-trunk"]], "Making a patch": [[54, "making-a-patch"]], "Making patches": [[54, "making-patches"]], "Moving from patching to development": [[54, "moving-from-patching-to-development"]], "Set up your fork": [[55, "set-up-your-fork"]], "Clone your fork": [[55, "clone-your-fork"]], "Linking your repository to the upstream repo": [[55, "linking-your-repository-to-the-upstream-repo"]], "Image voxel orientation": [[56, "image-voxel-orientation"]], "Images and memory": [[57, "images-and-memory"]], "Using in_memory to check the state of the cache": [[57, "using-in-memory-to-check-the-state-of-the-cache"]], "Using uncache": [[57, "using-uncache"]], "Saving memory": [[57, "saving-memory"]], "Uncache the array": [[57, "uncache-the-array"]], "Use the array proxy instead of get_fdata()": [[57, "use-the-array-proxy-instead-of-get-fdata"]], "Use the caching keyword to get_fdata()": [[57, "use-the-caching-keyword-to-get-fdata"]], "Saving time and memory": [[57, "saving-time-and-memory"]], "NiBabel": [[58, "nibabel"], [61, "nibabel"]], "Website": [[58, "website"], [69, "website"]], "Mailing Lists": [[58, "mailing-lists"], [69, "mailing-lists"]], "Code": [[58, "code"], [69, "code"]], "License": [[58, "license"], [69, "license"]], "Citing nibabel": [[58, "citing-nibabel"], [69, "citing-nibabel"]], "Authors and Contributors": [[58, "authors-and-contributors"]], "License reprise": [[58, "license-reprise"]], "Download and Installation": [[58, "download-and-installation"]], "Support": [[58, "support"]], "Installation": [[59, "installation"], [59, "id2"]], "Installer and packages": [[59, "installer-and-packages"]], "pip and the Python package index": [[59, "pip-and-the-python-package-index"]], "Debian/Ubuntu": [[59, "debian-ubuntu"]], "Install a development version": [[59, "install-a-development-version"]], "Requirements": [[59, "requirements"]], "Get the development sources": [[59, "get-the-development-sources"]], "Validating your install": [[59, "validating-your-install"]], "Installing data packages": [[60, "installing-data-packages"]], "Data package installation as an administrator": [[60, "data-package-installation-as-an-administrator"]], "Non-administrator data package installation": [[60, "non-administrator-data-package-installation"]], "On unix": [[60, "on-unix"]], "On windows": [[60, "on-windows"]], "Copyright and Licenses": [[61, "copyright-and-licenses"]], "3rd party code and data": [[61, "rd-party-code-and-data"]], "NetCDF": [[61, "netcdf"]], "Sphinx autosummary extension": [[61, "sphinx-autosummary-extension"]], "OrderedSet": [[61, "orderedset"]], "mni_icbm152_t1_tal_nlin_asym_09a": [[61, "mni-icbm152-t1-tal-nlin-asym-09a"]], "Philips PAR/REC data": [[61, "philips-par-rec-data"]], "NiBabel Manual": [[62, "nibabel-manual"]], "Radiological vs neurological conventions": [[63, "radiological-vs-neurological-conventions"]], "Neurological and radiological display convention": [[63, "neurological-and-radiological-display-convention"]], "Alignment of world and voxel axes": [[63, "alignment-of-world-and-voxel-axes"]], "Neurological / radiological voxel layout": [[63, "neurological-radiological-voxel-layout"]], "Nibabel images": [[64, "nibabel-images"]], "The image object": [[64, "the-image-object"]], "The image header": [[64, "the-image-header"]], "The image data array": [[64, "the-image-data-array"]], "Array proxies and proxy images": [[64, "array-proxies-and-proxy-images"]], "Getting the image data the easy way": [[64, "getting-the-image-data-the-easy-way"]], "Proxies and caching": [[64, "proxies-and-caching"]], "Image slicing": [[64, "image-slicing"]], "Loading and saving": [[64, "loading-and-saving"]], "Details of files and images": [[64, "details-of-files-and-images"]], "Working with NIfTI images": [[65, "working-with-nifti-images"]], "Preliminaries": [[65, "preliminaries"]], "Example NIfTI images": [[65, "example-nifti-images"]], "The NIfTI header": [[65, "the-nifti-header"]], "The NIfTI affines": [[65, "the-nifti-affines"]], "The sform affine": [[65, "the-sform-affine"]], "The qform affine": [[65, "the-qform-affine"]], "The fall-back header affine": [[65, "the-fall-back-header-affine"]], "Choosing the image affine": [[65, "choosing-the-image-affine"]], "Default sform and qform codes": [[65, "default-sform-and-qform-codes"]], "IPython notebooks for Nibabel project": [[66, "ipython-notebooks-for-nibabel-project"]], "Rotation matrix orthogonality": [[66, "rotation-matrix-orthogonality"]], "Relationship between images and io implementations": [[67, "relationship-between-images-and-io-implementations"]], "Summary and sign-off": [[67, "summary-and-sign-off"]], "Images": [[67, "images"]], "IO implementations": [[67, "io-implementations"]], "API Reference": [[68, "api-reference"]], "nibabel": [[69, "module-nibabel"]], "Quickstart": [[69, "quickstart"]], "bench": [[69, "bench"]], "get_info": [[69, "get-info"]], "test": [[69, "test"]], "affines": [[70, "module-nibabel.affines"]], "AffineError": [[70, "affineerror"]], "append_diag": [[70, "append-diag"]], "apply_affine": [[70, "apply-affine"]], "dot_reduce": [[70, "dot-reduce"]], "from_matvec": [[70, "from-matvec"]], "obliquity": [[70, "obliquity"]], "rescale_affine": [[70, "rescale-affine"]], "to_matvec": [[70, "to-matvec"]], "voxel_sizes": [[70, "voxel-sizes"]], "analyze": [[71, "module-nibabel.analyze"]], "The Analyze header format": [[71, "the-analyze-header-format"]], "Notes": [[71, "notes"], [76, "notes"]], "AnalyzeHeader": [[71, "analyzeheader"]], 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nibabel.freesurfer.io)": [[94, "nibabel.freesurfer.io.read_annot"]], "read_geometry() (in module nibabel.freesurfer.io)": [[94, "nibabel.freesurfer.io.read_geometry"]], "read_label() (in module nibabel.freesurfer.io)": [[94, "nibabel.freesurfer.io.read_label"]], "read_morph_data() (in module nibabel.freesurfer.io)": [[94, "nibabel.freesurfer.io.read_morph_data"]], "rw (nibabel.freesurfer.mghformat.mghimage attribute)": [[94, "nibabel.freesurfer.mghformat.MGHImage.rw"]], "set_data_dtype() (nibabel.freesurfer.mghformat.mghheader method)": [[94, "nibabel.freesurfer.mghformat.MGHHeader.set_data_dtype"]], "set_data_shape() (nibabel.freesurfer.mghformat.mghheader method)": [[94, "nibabel.freesurfer.mghformat.MGHHeader.set_data_shape"]], "set_zooms() (nibabel.freesurfer.mghformat.mghheader method)": [[94, "nibabel.freesurfer.mghformat.MGHHeader.set_zooms"]], "template_dtype (nibabel.freesurfer.mghformat.mghheader attribute)": [[94, "nibabel.freesurfer.mghformat.MGHHeader.template_dtype"]], 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"files_types (nibabel.gifti.gifti.giftiimage attribute)": [[96, "nibabel.gifti.gifti.GiftiImage.files_types"]], "flush_chardata() (nibabel.gifti.parse_gifti_fast.giftiimageparser method)": [[96, "nibabel.gifti.parse_gifti_fast.GiftiImageParser.flush_chardata"]], "from_dict() (nibabel.gifti.gifti.giftimetadata class method)": [[96, "nibabel.gifti.gifti.GiftiMetaData.from_dict"]], "from_file_map() (nibabel.gifti.gifti.giftiimage class method)": [[96, "nibabel.gifti.gifti.GiftiImage.from_file_map"]], "from_filename() (nibabel.gifti.gifti.giftiimage class method)": [[96, "nibabel.gifti.gifti.GiftiImage.from_filename"]], "get_arrays_from_intent() (nibabel.gifti.gifti.giftiimage method)": [[96, "nibabel.gifti.gifti.GiftiImage.get_arrays_from_intent"]], "get_labels_as_dict() (nibabel.gifti.gifti.giftilabeltable method)": [[96, "nibabel.gifti.gifti.GiftiLabelTable.get_labels_as_dict"]], "labeltable (nibabel.gifti.gifti.giftiimage property)": [[96, "nibabel.gifti.gifti.GiftiImage.labeltable"]], 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nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_acq_mat_txt"]], "get_b_matrix() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_b_matrix"]], "get_b_value() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_b_value"]], "get_csa_header() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_csa_header"]], "get_data() (nibabel.nicom.dicomwrappers.mosaicwrapper method)": [[104, "nibabel.nicom.dicomwrappers.MosaicWrapper.get_data"]], "get_data() (nibabel.nicom.dicomwrappers.multiframewrapper method)": [[104, "nibabel.nicom.dicomwrappers.MultiframeWrapper.get_data"]], "get_data() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.get_data"]], "get_g_vector() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_g_vector"]], "get_ice_dims() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_ice_dims"]], "get_n_mosaic() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_n_mosaic"]], "get_pixel_array() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.get_pixel_array"]], "get_scalar() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_scalar"]], "get_slice_normal() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_slice_normal"]], "get_vector() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.get_vector"]], "image_orient_patient() (nibabel.nicom.dicomwrappers.multiframewrapper method)": [[104, "nibabel.nicom.dicomwrappers.MultiframeWrapper.image_orient_patient"]], "image_orient_patient() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.image_orient_patient"]], "image_position() (nibabel.nicom.dicomwrappers.mosaicwrapper method)": [[104, "nibabel.nicom.dicomwrappers.MosaicWrapper.image_position"]], "image_position() (nibabel.nicom.dicomwrappers.multiframewrapper method)": [[104, "nibabel.nicom.dicomwrappers.MultiframeWrapper.image_position"]], "image_position() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.image_position"]], "image_shape() (nibabel.nicom.dicomwrappers.mosaicwrapper method)": [[104, "nibabel.nicom.dicomwrappers.MosaicWrapper.image_shape"]], "image_shape() (nibabel.nicom.dicomwrappers.multiframewrapper method)": [[104, "nibabel.nicom.dicomwrappers.MultiframeWrapper.image_shape"]], "image_shape() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.image_shape"]], "instance_number() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.instance_number"]], "is_csa (nibabel.nicom.dicomwrappers.siemenswrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.SiemensWrapper.is_csa"]], "is_csa (nibabel.nicom.dicomwrappers.wrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.is_csa"]], "is_mosaic (nibabel.nicom.dicomwrappers.mosaicwrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.MosaicWrapper.is_mosaic"]], "is_mosaic (nibabel.nicom.dicomwrappers.wrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.is_mosaic"]], "is_mosaic() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.is_mosaic"]], "is_multiframe (nibabel.nicom.dicomwrappers.multiframewrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.MultiframeWrapper.is_multiframe"]], "is_multiframe (nibabel.nicom.dicomwrappers.wrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.is_multiframe"]], "is_same_series() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.is_same_series"]], "mosaic_to_nii() (in module nibabel.nicom.dicomreaders)": [[104, "nibabel.nicom.dicomreaders.mosaic_to_nii"]], "nearest_pos_semi_def() (in module nibabel.nicom.dwiparams)": [[104, 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"nibabel.nicom.ascconv.parse_ascconv"]], "q2bg() (in module nibabel.nicom.dwiparams)": [[104, "nibabel.nicom.dwiparams.q2bg"]], "q_vector (nibabel.nicom.dicomwrappers.wrapper attribute)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.q_vector"]], "q_vector() (nibabel.nicom.dicomwrappers.siemenswrapper method)": [[104, "nibabel.nicom.dicomwrappers.SiemensWrapper.q_vector"]], "read() (in module nibabel.nicom.csareader)": [[104, "nibabel.nicom.csareader.read"]], "read() (nibabel.nicom.structreader.unpacker method)": [[104, "nibabel.nicom.structreader.Unpacker.read"]], "read_mosaic_dir() (in module nibabel.nicom.dicomreaders)": [[104, "nibabel.nicom.dicomreaders.read_mosaic_dir"]], "read_mosaic_dwi_dir() (in module nibabel.nicom.dicomreaders)": [[104, "nibabel.nicom.dicomreaders.read_mosaic_dwi_dir"]], "rotation_matrix() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.rotation_matrix"]], "series_signature() (nibabel.nicom.dicomwrappers.multiframewrapper method)": [[104, "nibabel.nicom.dicomwrappers.MultiframeWrapper.series_signature"]], "series_signature() (nibabel.nicom.dicomwrappers.siemenswrapper method)": [[104, "nibabel.nicom.dicomwrappers.SiemensWrapper.series_signature"]], "series_signature() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.series_signature"]], "slice_indicator() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.slice_indicator"]], "slice_normal() (nibabel.nicom.dicomwrappers.siemenswrapper method)": [[104, "nibabel.nicom.dicomwrappers.SiemensWrapper.slice_normal"]], "slice_normal() (nibabel.nicom.dicomwrappers.wrapper method)": [[104, "nibabel.nicom.dicomwrappers.Wrapper.slice_normal"]], "slices_to_series() (in module nibabel.nicom.dicomreaders)": [[104, "nibabel.nicom.dicomreaders.slices_to_series"]], "unpack() (nibabel.nicom.structreader.unpacker method)": [[104, 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"nifti1pair (class in nibabel.nifti1)": [[105, "nibabel.nifti1.Nifti1Pair"]], "nifti1pairheader (class in nibabel.nifti1)": [[105, "nibabel.nifti1.Nifti1PairHeader"]], "__init__() (nibabel.nifti1.nifti1dicomextension method)": [[105, "nibabel.nifti1.Nifti1DicomExtension.__init__"]], "__init__() (nibabel.nifti1.nifti1extension method)": [[105, "nibabel.nifti1.Nifti1Extension.__init__"]], "__init__() (nibabel.nifti1.nifti1extensions method)": [[105, "nibabel.nifti1.Nifti1Extensions.__init__"]], "__init__() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.__init__"]], "__init__() (nibabel.nifti1.nifti1image method)": [[105, "nibabel.nifti1.Nifti1Image.__init__"]], "__init__() (nibabel.nifti1.nifti1pair method)": [[105, "nibabel.nifti1.Nifti1Pair.__init__"]], "__init__() (nibabel.nifti1.nifti1pairheader method)": [[105, "nibabel.nifti1.Nifti1PairHeader.__init__"]], "as_reoriented() (nibabel.nifti1.nifti1pair method)": [[105, "nibabel.nifti1.Nifti1Pair.as_reoriented"]], "copy() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.copy"]], "count() (nibabel.nifti1.nifti1extensions method)": [[105, "nibabel.nifti1.Nifti1Extensions.count"]], "default_structarr() (nibabel.nifti1.nifti1header class method)": [[105, "nibabel.nifti1.Nifti1Header.default_structarr"]], "exts_klass (nibabel.nifti1.nifti1header attribute)": [[105, "nibabel.nifti1.Nifti1Header.exts_klass"]], "files_types (nibabel.nifti1.nifti1image attribute)": [[105, "nibabel.nifti1.Nifti1Image.files_types"]], "from_fileobj() (nibabel.nifti1.nifti1extensions class method)": [[105, "nibabel.nifti1.Nifti1Extensions.from_fileobj"]], "from_fileobj() (nibabel.nifti1.nifti1header class method)": [[105, "nibabel.nifti1.Nifti1Header.from_fileobj"]], "from_header() (nibabel.nifti1.nifti1header class method)": [[105, "nibabel.nifti1.Nifti1Header.from_header"]], "get_best_affine() (nibabel.nifti1.nifti1header method)": [[105, 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"nibabel.nifti1.Nifti1Header.set_dim_info"]], "set_intent() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.set_intent"]], "set_qform() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.set_qform"]], "set_qform() (nibabel.nifti1.nifti1pair method)": [[105, "nibabel.nifti1.Nifti1Pair.set_qform"]], "set_sform() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.set_sform"]], "set_sform() (nibabel.nifti1.nifti1pair method)": [[105, "nibabel.nifti1.Nifti1Pair.set_sform"]], "set_slice_duration() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.set_slice_duration"]], "set_slice_times() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.set_slice_times"]], "set_slope_inter() (nibabel.nifti1.nifti1header method)": [[105, "nibabel.nifti1.Nifti1Header.set_slope_inter"]], "set_xyzt_units() (nibabel.nifti1.nifti1header method)": [[105, 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"nibabel.nifti2.Nifti2Header.default_structarr"]], "get_data_shape() (nibabel.nifti2.nifti2header method)": [[106, "nibabel.nifti2.Nifti2Header.get_data_shape"]], "header_class (nibabel.nifti2.nifti2image attribute)": [[106, "nibabel.nifti2.Nifti2Image.header_class"]], "header_class (nibabel.nifti2.nifti2pair attribute)": [[106, "nibabel.nifti2.Nifti2Pair.header_class"]], "is_single (nibabel.nifti2.nifti2pairheader attribute)": [[106, "nibabel.nifti2.Nifti2PairHeader.is_single"]], "load() (in module nibabel.nifti2)": [[106, "nibabel.nifti2.load"]], "may_contain_header() (nibabel.nifti2.nifti2header class method)": [[106, "nibabel.nifti2.Nifti2Header.may_contain_header"]], "nibabel.nifti2": [[106, "module-nibabel.nifti2"]], "pair_magic (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.pair_magic"]], "pair_vox_offset (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.pair_vox_offset"]], "quaternion_threshold (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.quaternion_threshold"]], "save() (in module nibabel.nifti2)": [[106, "nibabel.nifti2.save"]], "set_data_shape() (nibabel.nifti2.nifti2header method)": [[106, "nibabel.nifti2.Nifti2Header.set_data_shape"]], "single_magic (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.single_magic"]], "single_vox_offset (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.single_vox_offset"]], "sizeof_hdr (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.sizeof_hdr"]], "template_dtype (nibabel.nifti2.nifti2header attribute)": [[106, "nibabel.nifti2.Nifti2Header.template_dtype"]], "onetimeproperty (class in nibabel.onetime)": [[107, "nibabel.onetime.OneTimeProperty"]], "resetmixin (class in nibabel.onetime)": [[107, "nibabel.onetime.ResetMixin"]], "__init__() (nibabel.onetime.onetimeproperty method)": [[107, 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"nibabel.openers.Opener.__init__"]], "bz2_def (nibabel.openers.opener attribute)": [[108, "nibabel.openers.Opener.bz2_def"]], "close() (nibabel.openers.opener method)": [[108, "nibabel.openers.Opener.close"]], "close_if_mine() (nibabel.openers.opener method)": [[108, "nibabel.openers.Opener.close_if_mine"]], "closed (nibabel.openers.opener property)": [[108, "nibabel.openers.Opener.closed"]], "compress_ext_icase (nibabel.openers.opener attribute)": [[108, "nibabel.openers.Opener.compress_ext_icase"]], "compress_ext_map (nibabel.openers.imageopener attribute)": [[108, "nibabel.openers.ImageOpener.compress_ext_map"]], "compress_ext_map (nibabel.openers.opener attribute)": [[108, "nibabel.openers.Opener.compress_ext_map"]], "default_compresslevel (nibabel.openers.opener attribute)": [[108, "nibabel.openers.Opener.default_compresslevel"]], "default_level_or_option (nibabel.openers.opener attribute)": [[108, "nibabel.openers.Opener.default_level_or_option"]], "default_zst_compresslevel 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"nibabel.optpkg": [[109, "module-nibabel.optpkg"]], "optional_package() (in module nibabel.optpkg)": [[109, "nibabel.optpkg.optional_package"]], "orientationerror (class in nibabel.orientations)": [[110, "nibabel.orientations.OrientationError"]], "__init__() (nibabel.orientations.orientationerror method)": [[110, "nibabel.orientations.OrientationError.__init__"]], "aff2axcodes() (in module nibabel.orientations)": [[110, "nibabel.orientations.aff2axcodes"]], "apply_orientation() (in module nibabel.orientations)": [[110, "nibabel.orientations.apply_orientation"]], "axcodes2ornt() (in module nibabel.orientations)": [[110, "nibabel.orientations.axcodes2ornt"]], "flip_axis() (in module nibabel.orientations)": [[110, "nibabel.orientations.flip_axis"]], "inv_ornt_aff() (in module nibabel.orientations)": [[110, "nibabel.orientations.inv_ornt_aff"]], "io_orientation() (in module nibabel.orientations)": [[110, "nibabel.orientations.io_orientation"]], "nibabel.orientations": [[110, 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"nibabel.parrec.PARRECHeader.from_header"]], "get_affine() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_affine"]], "get_bvals_bvecs() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_bvals_bvecs"]], "get_data_offset() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_data_offset"]], "get_data_scaling() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_data_scaling"]], "get_def() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_def"]], "get_echo_train_length() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_echo_train_length"]], "get_q_vectors() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_q_vectors"]], "get_rec_shape() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.get_rec_shape"]], "get_slice_orientation() (nibabel.parrec.parrecheader method)": 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property)": [[111, "nibabel.parrec.PARRECArrayProxy.ndim"]], "nibabel.parrec": [[111, "module-nibabel.parrec"]], "one_line() (in module nibabel.parrec)": [[111, "nibabel.parrec.one_line"]], "parse_par_header() (in module nibabel.parrec)": [[111, "nibabel.parrec.parse_PAR_header"]], "rw (nibabel.parrec.parrecimage attribute)": [[111, "nibabel.parrec.PARRECImage.rw"]], "set_data_offset() (nibabel.parrec.parrecheader method)": [[111, "nibabel.parrec.PARRECHeader.set_data_offset"]], "shape (nibabel.parrec.parrecarrayproxy property)": [[111, "nibabel.parrec.PARRECArrayProxy.shape"]], "valid_exts (nibabel.parrec.parrecimage attribute)": [[111, "nibabel.parrec.PARRECImage.valid_exts"]], "vol_is_full() (in module nibabel.parrec)": [[111, "nibabel.parrec.vol_is_full"]], "vol_numbers() (in module nibabel.parrec)": [[111, "nibabel.parrec.vol_numbers"]], "adapt_affine() (in module nibabel.processing)": [[112, "nibabel.processing.adapt_affine"]], "conform() (in module nibabel.processing)": [[112, 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module nibabel.quaternions)": [[114, "nibabel.quaternions.rotate_vector"]], "nibabel.rstutils": [[115, "module-nibabel.rstutils"]], "rst_table() (in module nibabel.rstutils)": [[115, "nibabel.rstutils.rst_table"]], "nibabel.spaces": [[116, "module-nibabel.spaces"]], "slice2volume() (in module nibabel.spaces)": [[116, "nibabel.spaces.slice2volume"]], "vox2out_vox() (in module nibabel.spaces)": [[116, "nibabel.spaces.vox2out_vox"]], "headerdataerror (class in nibabel.spatialimages)": [[117, "nibabel.spatialimages.HeaderDataError"]], "headertypeerror (class in nibabel.spatialimages)": [[117, "nibabel.spatialimages.HeaderTypeError"]], "imagedataerror (class in nibabel.spatialimages)": [[117, "nibabel.spatialimages.ImageDataError"]], "imageslicer (nibabel.spatialimages.spatialimage attribute)": [[117, "nibabel.spatialimages.SpatialImage.ImageSlicer"]], "spatialfirstslicer (class in nibabel.spatialimages)": [[117, "nibabel.spatialimages.SpatialFirstSlicer"]], "spatialheader (class in nibabel.spatialimages)": [[117, "nibabel.spatialimages.SpatialHeader"]], "spatialimage (class in nibabel.spatialimages)": [[117, "nibabel.spatialimages.SpatialImage"]], "__init__() (nibabel.spatialimages.headerdataerror method)": [[117, "nibabel.spatialimages.HeaderDataError.__init__"]], "__init__() (nibabel.spatialimages.headertypeerror method)": [[117, "nibabel.spatialimages.HeaderTypeError.__init__"]], "__init__() (nibabel.spatialimages.imagedataerror method)": [[117, "nibabel.spatialimages.ImageDataError.__init__"]], "__init__() (nibabel.spatialimages.spatialfirstslicer method)": [[117, "nibabel.spatialimages.SpatialFirstSlicer.__init__"]], "__init__() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.__init__"]], "__init__() (nibabel.spatialimages.spatialimage method)": [[117, "nibabel.spatialimages.SpatialImage.__init__"]], "affine (nibabel.spatialimages.spatialimage property)": [[117, "nibabel.spatialimages.SpatialImage.affine"]], "as_reoriented() (nibabel.spatialimages.spatialimage method)": [[117, "nibabel.spatialimages.SpatialImage.as_reoriented"]], "check_slicing() (nibabel.spatialimages.spatialfirstslicer method)": [[117, "nibabel.spatialimages.SpatialFirstSlicer.check_slicing"]], "copy() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.copy"]], "data_from_fileobj() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.data_from_fileobj"]], "data_layout (nibabel.spatialimages.spatialheader attribute)": [[117, "nibabel.spatialimages.SpatialHeader.data_layout"]], "data_to_fileobj() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.data_to_fileobj"]], "default_x_flip (nibabel.spatialimages.spatialheader attribute)": [[117, "nibabel.spatialimages.SpatialHeader.default_x_flip"]], "from_fileobj() (nibabel.spatialimages.spatialheader class method)": [[117, "nibabel.spatialimages.SpatialHeader.from_fileobj"]], "from_header() (nibabel.spatialimages.spatialheader class method)": [[117, "nibabel.spatialimages.SpatialHeader.from_header"]], "from_image() (nibabel.spatialimages.spatialimage class method)": [[117, "nibabel.spatialimages.SpatialImage.from_image"]], "get_base_affine() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.get_base_affine"]], "get_best_affine() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.get_best_affine"]], "get_data_dtype() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.get_data_dtype"]], "get_data_dtype() (nibabel.spatialimages.spatialimage method)": [[117, "nibabel.spatialimages.SpatialImage.get_data_dtype"]], "get_data_shape() (nibabel.spatialimages.spatialheader method)": [[117, "nibabel.spatialimages.SpatialHeader.get_data_shape"]], "get_zooms() (nibabel.spatialimages.spatialheader 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