API Reference

• nibabel
  • Website
  • Mailing Lists
  • Code
  • License
  • Citing nibabel
  • Quickstart
  • get_info
  • setup_package
  • teardown_package
• _h5py_compat
• affines
  • AffineError
  • append_diag
  • apply_affine
  • dot_reduce
  • from_matvec
  • to_matvec
  • voxel_sizes
• analyze
  • The Analyze header format
    • Notes
  • AnalyzeHeader
  • AnalyzeImage
• arrayproxy
  • ArrayProxy
  • is_proxy
  • reshape_dataobj
• arraywriters
  • ArrayWriter
  • ScalingError
  • SlopeArrayWriter
  • SlopeInterArrayWriter
  • WriterError
  • get_slope_inter
  • make_array_writer
• batteryrunners
  • More about checks
  • BatteryRunner
  • Report
• benchmarks
  • Module: benchmarks.bench_array_to_file
  • Module: benchmarks.bench_arrayproxy_slicing
  • Module: benchmarks.bench_fileslice
  • Module: benchmarks.bench_finite_range
  • Module: benchmarks.bench_load_save
  • Module: benchmarks.bench_streamlines
  • Module: benchmarks.butils
    • bench_array_to_file
    • bench_arrayproxy_slicing
    • bench_fileslice
    • run_slices
    • bench_finite_range
    • bench_load_save
    • bench_load_trk
    • print_git_title
• brikhead
  • Notes
  • AFNIArrayProxy
  • AFNIHeader
  • AFNIHeaderError
  • AFNIImage
  • AFNIImageError
  • parse_AFNI_header
• casting
  • CastingError
  • FloatingError
  • able_int_type
  • as_int
  • best_float
  • ceil_exact
  • float_to_int
  • floor_exact
  • floor_log2
  • have_binary128
  • int_abs
  • int_to_float
  • longdouble_lte_float64
  • longdouble_precision_improved
  • ok_floats
  • on_powerpc
  • shared_range
  • type_info
  • ulp
• checkwarns
  • ErrorWarnings
  • IgnoreWarnings
• cifti2
  • Module: cifti2.cifti2
  • Module: cifti2.cifti2_axes
    • Creating new CIFTI-2 axes
    • Examples
  • Module: cifti2.parse_cifti2
    • Cifti2BrainModel
    • Cifti2Header
    • Cifti2HeaderError
    • Cifti2Image
    • Cifti2Label
    • Cifti2LabelTable
    • Cifti2Matrix
    • Cifti2MatrixIndicesMap
    • Cifti2MetaData
    • Cifti2NamedMap
    • Cifti2Parcel
    • Cifti2Surface
    • Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ
    • Cifti2VertexIndices
    • Cifti2Vertices
    • Cifti2Volume
    • Cifti2VoxelIndicesIJK
    • Axis
    • BrainModelAxis
    • LabelAxis
    • ParcelsAxis
    • ScalarAxis
    • SeriesAxis
    • from_index_mapping
    • to_header
    • Cifti2Extension
    • Cifti2Parser
• cmdline
  • Module: cmdline.dicomfs
  • Module: cmdline.diff
  • Module: cmdline.ls
  • Module: cmdline.nifti_dx
  • Module: cmdline.parrec2nii
  • Module: cmdline.tck2trk
  • Module: cmdline.trk2tck
  • Module: cmdline.utils
    • DICOMFS
    • FileHandle
    • dummy_fuse
    • get_opt_parser
    • main
    • are_values_different
    • diff
    • display_diff
    • get_data_diff
    • get_data_hash_diff
    • get_headers_diff
    • get_opt_parser
    • main
    • get_opt_parser
    • main
    • proc_file
    • main
    • error
    • get_opt_parser
    • main
    • proc_file
    • verbose
    • main
    • parse_args
    • main
    • parse_args
    • ap
    • safe_get
    • table2string
    • verbose
• data
  • Bomber
  • BomberError
  • DataError
  • Datasource
  • VersionedDatasource
  • datasource_or_bomber
  • find_data_dir
  • get_data_path
  • make_datasource
• dataobj_images
  • DataobjImage
• deprecated
  • FutureWarningMixin
  • ModuleProxy
  • VisibleDeprecationWarning
• deprecator
  • Deprecator
  • ExpiredDeprecationError
• dft
  • CachingError
  • DFTError
  • InstanceStackError
  • VolumeError
  • clear_cache
  • get_studies
  • update_cache
• ecat
  • EcatHeader
  • EcatImage
  • EcatImageArrayProxy
  • EcatSubHeader
  • get_frame_order
  • get_series_framenumbers
  • read_mlist
  • read_subheaders
• environment
  • get_home_dir
  • get_nipy_system_dir
  • get_nipy_user_dir
• eulerangles
  • angle_axis2euler
  • euler2angle_axis
  • euler2mat
  • euler2quat
  • mat2euler
  • quat2euler
• filebasedimages
  • FileBasedHeader
  • FileBasedImage
  • ImageFileError
  • SerializableImage
• fileholders
  • FileHolder
  • FileHolderError
  • copy_file_map
• filename_parser
  • TypesFilenamesError
  • parse_filename
  • splitext_addext
  • types_filenames
• fileslice
  • calc_slicedefs
  • canonical_slicers
  • fileslice
  • fill_slicer
  • is_fancy
  • optimize_read_slicers
  • optimize_slicer
  • predict_shape
  • read_segments
  • slice2len
  • slice2outax
  • slicers2segments
  • strided_scalar
  • threshold_heuristic
• fileutils
  • read_zt_byte_strings
• freesurfer
  • Module: freesurfer.io
  • Module: freesurfer.mghformat
    • read_annot
    • read_geometry
    • read_label
    • read_morph_data
    • write_annot
    • write_geometry
    • write_morph_data
    • MGHError
    • MGHHeader
    • MGHImage
• funcs
  • as_closest_canonical
  • concat_images
  • four_to_three
  • squeeze_image
• gifti
  • Module: gifti.gifti
  • Module: gifti.giftiio
  • Module: gifti.parse_gifti_fast
  • Module: gifti.util
    • GiftiCoordSystem
    • GiftiDataArray
    • GiftiImage
    • GiftiLabel
    • GiftiLabelTable
    • GiftiMetaData
    • GiftiNVPairs
    • data_tag
    • read
    • write
    • GiftiImageParser
    • GiftiParseError
    • Outputter
    • parse_gifti_file
    • read_data_block
• imageclasses
  • ClassMapDict
  • ExtMapRecoder
  • spatial_axes_first
• imageglobals
  • ErrorLevel
  • LoggingOutputSuppressor
• keywordonly
  • kw_only_func
  • kw_only_meth
• loadsave
  • guessed_image_type
  • load
  • read_img_data
  • save
  • which_analyze_type
• minc
• minc1
  • Minc1File
  • Minc1Header
  • Minc1Image
  • MincError
  • MincHeader
  • MincImageArrayProxy
  • MincFile
  • MincImage
• minc2
  • Hdf5Bunch
  • Minc2File
  • Minc2Header
  • Minc2Image
• mriutils
  • MRIError
  • calculate_dwell_time
• nicom
  • Module: nicom.csareader
  • Module: nicom.dicomreaders
  • Module: nicom.dicomwrappers
  • Module: nicom.dwiparams
  • Module: nicom.structreader
  • Module: nicom.utils
    • CSAError
    • CSAReadError
    • get_acq_mat_txt
    • get_b_matrix
    • get_b_value
    • get_csa_header
    • get_g_vector
    • get_ice_dims
    • get_n_mosaic
    • get_scalar
    • get_slice_normal
    • get_vector
    • is_mosaic
    • nt_str
    • read
    • DicomReadError
    • mosaic_to_nii
    • read_mosaic_dir
    • read_mosaic_dwi_dir
    • slices_to_series
    • MosaicWrapper
    • MultiframeWrapper
    • SiemensWrapper
    • Wrapper
    • WrapperError
    • WrapperPrecisionError
    • none_or_close
    • wrapper_from_data
    • wrapper_from_file
    • B2q
    • nearest_pos_semi_def
    • q2bg
    • Unpacker
    • find_private_section
• nifti1
  • Nifti1DicomExtension
  • Nifti1Extension
  • Nifti1Extensions
  • Nifti1Header
  • Nifti1Image
  • Nifti1Pair
  • Nifti1PairHeader
  • load
  • save
• nifti2
  • Nifti2Header
  • Nifti2Image
  • Nifti2Pair
  • Nifti2PairHeader
  • load
  • save
• onetime
  • References
  • OneTimeProperty
  • ResetMixin
  • auto_attr
  • setattr_on_read
• openers
  • BufferedGzipFile
  • ImageOpener
  • Opener
• optpkg
  • optional_package
• orientations
  • OrientationError
  • aff2axcodes
  • apply_orientation
  • axcodes2ornt
  • flip_axis
  • inv_ornt_aff
  • io_orientation
  • orientation_affine
  • ornt2axcodes
  • ornt_transform
• parrec
  • PAR file format
    • General information
    • Image information
    • Orientation
    • Data type
    • Data Sorting
  • PARRECArrayProxy
  • PARRECError
  • PARRECHeader
  • PARRECImage
  • exts2pars
  • one_line
  • parse_PAR_header
  • vol_is_full
  • vol_numbers
• processing
  • adapt_affine
  • fwhm2sigma
  • resample_from_to
  • resample_to_output
  • sigma2fwhm
  • smooth_image
• py3k
  • asbytes
  • asbytes_nested
  • asstr
  • asunicode_nested
  • getexception
  • ints2bytes
  • isfileobj
  • open_latin1
• pydicom_compat
• quaternions
  • angle_axis2mat
  • angle_axis2quat
  • conjugate
  • eye
  • fillpositive
  • inverse
  • isunit
  • mat2quat
  • mult
  • nearly_equivalent
  • norm
  • quat2angle_axis
  • quat2mat
  • rotate_vector
• rstutils
  • rst_table
• spaces
  • slice2volume
  • vox2out_vox
• spatialimages
  • There are several ways of writing data.
  • Files interface
  • Header
  • HeaderDataError
  • HeaderTypeError
  • ImageDataError
  • SpatialFirstSlicer
  • SpatialHeader
  • SpatialImage
  • supported_np_types
• spm2analyze
  • Spm2AnalyzeHeader
  • Spm2AnalyzeImage
• spm99analyze
  • Spm99AnalyzeHeader
  • Spm99AnalyzeImage
  • SpmAnalyzeHeader
• streamlines
  • Module: streamlines.array_sequence
  • Module: streamlines.header
  • Module: streamlines.tck
  • Module: streamlines.tractogram
  • Module: streamlines.tractogram_file
  • Module: streamlines.trk
  • Module: streamlines.utils
    • detect_format
    • is_supported
    • load
    • save
    • ArraySequence
    • concatenate
    • create_arraysequences_from_generator
    • is_array_sequence
    • is_ndarray_of_int_or_bool
    • Field
    • TckFile
    • LazyDict
    • LazyTractogram
    • PerArrayDict
    • PerArraySequenceDict
    • SliceableDataDict
    • Tractogram
    • TractogramItem
    • is_data_dict
    • is_lazy_dict
    • DataError
    • DataWarning
    • ExtensionWarning
    • HeaderError
    • HeaderWarning
    • TractogramFile
    • abstractclassmethod
    • TrkFile
    • decode_value_from_name
    • encode_value_in_name
    • get_affine_rasmm_to_trackvis
    • get_affine_trackvis_to_rasmm
    • get_affine_from_reference
    • peek_next
• tmpdirs
  • InGivenDirectory
  • InTemporaryDirectory
  • TemporaryDirectory
• trackvis
  • DataError
  • HeaderError
  • TrackvisFile
  • TrackvisFileError
  • aff_from_hdr
  • aff_to_hdr
  • empty_header
  • read
  • write
• tripwire
  • TripWire
  • TripWireError
  • is_tripwire
• viewers
  • OrthoSlicer3D
• volumeutils
  • BinOpener
  • DtypeMapper
  • Recoder
  • allopen
  • apply_read_scaling
  • array_from_file
  • array_to_file
  • best_write_scale_ftype
  • better_float_of
  • calculate_scale
  • can_cast
  • finite_range
  • fname_ext_ul_case
  • int_scinter_ftype
  • make_dt_codes
  • pretty_mapping
  • rec2dict
  • scale_min_max
  • seek_tell
  • shape_zoom_affine
  • working_type
  • write_zeros
• wrapstruct
  • wrapstruct
    • Mappingness
    • Consistency checks
  • LabeledWrapStruct
  • WrapStruct
  • WrapStructError
• xmlutils
  • XmlBasedHeader
  • XmlParser
  • XmlSerializable