API ReferenceΒΆ
nibabel
_compression
affines
analyze
- The Analyze header format
AnalyzeHeader
AnalyzeHeader
AnalyzeHeader.__init__()
AnalyzeHeader.as_analyze_map()
AnalyzeHeader.data_from_fileobj()
AnalyzeHeader.data_to_fileobj()
AnalyzeHeader.default_structarr()
AnalyzeHeader.default_x_flip
AnalyzeHeader.from_header()
AnalyzeHeader.get_base_affine()
AnalyzeHeader.get_best_affine()
AnalyzeHeader.get_data_dtype()
AnalyzeHeader.get_data_offset()
AnalyzeHeader.get_data_shape()
AnalyzeHeader.get_slope_inter()
AnalyzeHeader.get_zooms()
AnalyzeHeader.guessed_endian()
AnalyzeHeader.has_data_intercept
AnalyzeHeader.has_data_slope
AnalyzeHeader.may_contain_header()
AnalyzeHeader.raw_data_from_fileobj()
AnalyzeHeader.set_data_dtype()
AnalyzeHeader.set_data_offset()
AnalyzeHeader.set_data_shape()
AnalyzeHeader.set_slope_inter()
AnalyzeHeader.set_zooms()
AnalyzeHeader.sizeof_hdr
AnalyzeHeader.template_dtype
AnalyzeImage
arrayproxy
arraywriters
batteryrunners
benchmarks
brikhead
caret
casting
cifti2
- Module:
cifti2.cifti2
- Module:
cifti2.cifti2_axes
- Module:
cifti2.parse_cifti2
Cifti2BrainModel
Cifti2Header
Cifti2HeaderError
Cifti2Image
Cifti2Image
Cifti2Image.__init__()
Cifti2Image.files_types
Cifti2Image.from_file_map()
Cifti2Image.from_image()
Cifti2Image.get_data_dtype()
Cifti2Image.header_class
Cifti2Image.makeable
Cifti2Image.nifti_header
Cifti2Image.rw
Cifti2Image.set_data_dtype()
Cifti2Image.to_file_map()
Cifti2Image.update_headers()
Cifti2Image.valid_exts
Cifti2Label
Cifti2LabelTable
Cifti2Matrix
Cifti2MatrixIndicesMap
Cifti2MetaData
Cifti2NamedMap
Cifti2Parcel
Cifti2Surface
Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ
Cifti2VertexIndices
Cifti2Vertices
Cifti2Volume
Cifti2VoxelIndicesIJK
LimitedNifti2Header
Axis
BrainModelAxis
BrainModelAxis
BrainModelAxis.__init__()
BrainModelAxis.affine
BrainModelAxis.from_index_mapping()
BrainModelAxis.from_mask()
BrainModelAxis.from_surface()
BrainModelAxis.get_element()
BrainModelAxis.iter_structures()
BrainModelAxis.name
BrainModelAxis.surface_mask
BrainModelAxis.to_cifti_brain_structure_name()
BrainModelAxis.to_mapping()
BrainModelAxis.volume_mask
BrainModelAxis.volume_shape
LabelAxis
ParcelsAxis
ScalarAxis
SeriesAxis
- from_index_mapping
- to_header
Cifti2Extension
Cifti2Parser
- Module:
cmdline
- Module:
cmdline.conform
- Module:
cmdline.convert
- Module:
cmdline.dicomfs
- Module:
cmdline.diff
- Module:
cmdline.ls
- Module:
cmdline.nifti_dx
- Module:
cmdline.parrec2nii
- Module:
cmdline.roi
- Module:
cmdline.stats
- Module:
cmdline.tck2trk
- Module:
cmdline.trk2tck
- Module:
cmdline.utils
- main
- main
DICOMFS
FileHandle
dummy_fuse
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
- lossless_slice
- main
- parse_slice
- sanitize
- main
- main
- parse_args
- main
- parse_args
- ap
- safe_get
- table2string
- verbose
- Module:
data
dataobj_images
deprecated
deprecator
dft
ecat
EcatHeader
EcatImage
EcatImage
EcatImage.__init__()
EcatImage.ImageArrayProxy
EcatImage.affine
EcatImage.files_types
EcatImage.from_file_map()
EcatImage.from_image()
EcatImage.get_data_dtype()
EcatImage.get_frame()
EcatImage.get_frame_affine()
EcatImage.get_mlist()
EcatImage.get_subheaders()
EcatImage.header_class
EcatImage.load()
EcatImage.shape
EcatImage.subheader_class
EcatImage.to_file_map()
EcatImage.valid_exts
EcatImageArrayProxy
EcatSubHeader
- get_frame_order
- get_series_framenumbers
- read_mlist
- read_subheaders
environment
eulerangles
filebasedimages
FileBasedHeader
FileBasedImage
FileBasedImage
FileBasedImage.__init__()
FileBasedImage.files_types
FileBasedImage.filespec_to_file_map()
FileBasedImage.from_file_map()
FileBasedImage.from_filename()
FileBasedImage.from_image()
FileBasedImage.get_filename()
FileBasedImage.header
FileBasedImage.header_class
FileBasedImage.instance_to_filename()
FileBasedImage.load()
FileBasedImage.make_file_map()
FileBasedImage.makeable
FileBasedImage.path_maybe_image()
FileBasedImage.rw
FileBasedImage.set_filename()
FileBasedImage.to_file_map()
FileBasedImage.to_filename()
FileBasedImage.valid_exts
ImageFileError
SerializableImage
fileholders
filename_parser
fileslice
fileutils
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
MGHHeader
MGHHeader.__init__()
MGHHeader.as_byteswapped()
MGHHeader.chk_version()
MGHHeader.copy()
MGHHeader.data_from_fileobj()
MGHHeader.default_structarr()
MGHHeader.diagnose_binaryblock()
MGHHeader.from_fileobj()
MGHHeader.from_header()
MGHHeader.get_affine()
MGHHeader.get_best_affine()
MGHHeader.get_data_bytespervox()
MGHHeader.get_data_dtype()
MGHHeader.get_data_offset()
MGHHeader.get_data_shape()
MGHHeader.get_data_size()
MGHHeader.get_footer_offset()
MGHHeader.get_ras2vox()
MGHHeader.get_slope_inter()
MGHHeader.get_vox2ras()
MGHHeader.get_vox2ras_tkr()
MGHHeader.get_zooms()
MGHHeader.guessed_endian()
MGHHeader.set_data_dtype()
MGHHeader.set_data_shape()
MGHHeader.set_zooms()
MGHHeader.template_dtype
MGHHeader.writeftr_to()
MGHHeader.writehdr_to()
MGHImage
- Module:
funcs
gifti
- Module:
gifti.gifti
- Module:
gifti.parse_gifti_fast
- Module:
gifti.util
GiftiCoordSystem
GiftiDataArray
GiftiImage
GiftiImage
GiftiImage.__init__()
GiftiImage.add_gifti_data_array()
GiftiImage.agg_data()
GiftiImage.files_types
GiftiImage.from_file_map()
GiftiImage.from_filename()
GiftiImage.get_arrays_from_intent()
GiftiImage.labeltable
GiftiImage.meta
GiftiImage.numDA
GiftiImage.parser
GiftiImage.print_summary()
GiftiImage.remove_gifti_data_array()
GiftiImage.remove_gifti_data_array_by_intent()
GiftiImage.to_bytes()
GiftiImage.to_file_map()
GiftiImage.to_xml()
GiftiImage.valid_exts
GiftiLabel
GiftiLabelTable
GiftiMetaData
GiftiNVPairs
GiftiImageParser
GiftiParseError
- read_data_block
- Module:
imageclasses
imageglobals
imagestats
loadsave
minc1
minc2
mriutils
nicom
- Module:
nicom.ascconv
- Module:
nicom.csareader
- Module:
nicom.dicomreaders
- Module:
nicom.dicomwrappers
- Module:
nicom.dwiparams
- Module:
nicom.structreader
- Module:
nicom.utils
AscconvParseError
Atom
NoValue
- assign2atoms
- obj_from_atoms
- parse_ascconv
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
FilterDwiIso
FilterMultiStack
FrameFilter
MosaicWrapper
MultiframeWrapper
MultiframeWrapper
MultiframeWrapper.__init__()
MultiframeWrapper.frame_order
MultiframeWrapper.get_unscaled_data()
MultiframeWrapper.image_orient_patient
MultiframeWrapper.image_position
MultiframeWrapper.image_shape
MultiframeWrapper.is_multiframe
MultiframeWrapper.scale_factors
MultiframeWrapper.series_signature
MultiframeWrapper.vendor
MultiframeWrapper.voxel_sizes
SiemensWrapper
Wrapper
Wrapper
Wrapper.__init__()
Wrapper.affine
Wrapper.b_matrix
Wrapper.b_value
Wrapper.b_vector
Wrapper.get()
Wrapper.get_data()
Wrapper.get_pixel_array()
Wrapper.get_unscaled_data()
Wrapper.image_orient_patient
Wrapper.image_position
Wrapper.image_shape
Wrapper.instance_number
Wrapper.is_csa
Wrapper.is_mosaic
Wrapper.is_multiframe
Wrapper.is_same_series()
Wrapper.q_vector
Wrapper.rotation_matrix
Wrapper.scale_factors
Wrapper.series_signature
Wrapper.slice_indicator
Wrapper.slice_normal
Wrapper.vendor
Wrapper.voxel_sizes
WrapperError
WrapperPrecisionError
- none_or_close
- wrapper_from_data
- wrapper_from_file
- B2q
- nearest_pos_semi_def
- q2bg
Unpacker
Vendor
- find_private_section
- vendor_from_private
- Module:
nifti1
Nifti1DicomExtension
Nifti1Extension
Nifti1Extensions
Nifti1Header
Nifti1Header
Nifti1Header.__init__()
Nifti1Header.copy()
Nifti1Header.default_structarr()
Nifti1Header.exts_klass
Nifti1Header.from_fileobj()
Nifti1Header.from_header()
Nifti1Header.get_best_affine()
Nifti1Header.get_data_shape()
Nifti1Header.get_dim_info()
Nifti1Header.get_intent()
Nifti1Header.get_n_slices()
Nifti1Header.get_qform()
Nifti1Header.get_qform_quaternion()
Nifti1Header.get_sform()
Nifti1Header.get_slice_duration()
Nifti1Header.get_slice_times()
Nifti1Header.get_slope_inter()
Nifti1Header.get_xyzt_units()
Nifti1Header.has_data_intercept
Nifti1Header.has_data_slope
Nifti1Header.is_single
Nifti1Header.may_contain_header()
Nifti1Header.pair_magic
Nifti1Header.pair_vox_offset
Nifti1Header.quaternion_threshold
Nifti1Header.set_data_dtype()
Nifti1Header.set_data_shape()
Nifti1Header.set_dim_info()
Nifti1Header.set_intent()
Nifti1Header.set_qform()
Nifti1Header.set_sform()
Nifti1Header.set_slice_duration()
Nifti1Header.set_slice_times()
Nifti1Header.set_slope_inter()
Nifti1Header.set_xyzt_units()
Nifti1Header.single_magic
Nifti1Header.single_vox_offset
Nifti1Header.template_dtype
Nifti1Header.write_to()
Nifti1Image
Nifti1Pair
Nifti1PairHeader
NiftiExtension
NiftiExtension
NiftiExtension.__init__()
NiftiExtension.code
NiftiExtension.content
NiftiExtension.encoding
NiftiExtension.from_bytes()
NiftiExtension.from_object()
NiftiExtension.get_code()
NiftiExtension.get_content()
NiftiExtension.get_object()
NiftiExtension.get_sizeondisk()
NiftiExtension.json()
NiftiExtension.text
NiftiExtension.write_to()
- load
- save
nifti2
Nifti2Header
Nifti2Header
Nifti2Header.__init__()
Nifti2Header.default_structarr()
Nifti2Header.get_data_shape()
Nifti2Header.may_contain_header()
Nifti2Header.pair_magic
Nifti2Header.pair_vox_offset
Nifti2Header.quaternion_threshold
Nifti2Header.set_data_shape()
Nifti2Header.single_magic
Nifti2Header.single_vox_offset
Nifti2Header.sizeof_hdr
Nifti2Header.template_dtype
Nifti2Image
Nifti2Pair
Nifti2PairHeader
- load
- save
onetime
openers
DeterministicGzipFile
Fileish
ImageOpener
Opener
Opener
Opener.__init__()
Opener.bz2_def
Opener.close()
Opener.close_if_mine()
Opener.closed
Opener.compress_ext_icase
Opener.compress_ext_map
Opener.default_compresslevel
Opener.default_level_or_option
Opener.default_zst_compresslevel
Opener.fileno()
Opener.fobj
Opener.gz_def
Opener.mode
Opener.name
Opener.read()
Opener.readinto()
Opener.seek()
Opener.tell()
Opener.write()
Opener.zstd_def
optpkg
orientations
parrec
- PAR file format
PARRECArrayProxy
PARRECError
PARRECHeader
PARRECHeader
PARRECHeader.__init__()
PARRECHeader.as_analyze_map()
PARRECHeader.copy()
PARRECHeader.from_fileobj()
PARRECHeader.from_header()
PARRECHeader.get_affine()
PARRECHeader.get_bvals_bvecs()
PARRECHeader.get_data_offset()
PARRECHeader.get_data_scaling()
PARRECHeader.get_def()
PARRECHeader.get_echo_train_length()
PARRECHeader.get_q_vectors()
PARRECHeader.get_rec_shape()
PARRECHeader.get_slice_orientation()
PARRECHeader.get_sorted_slice_indices()
PARRECHeader.get_volume_labels()
PARRECHeader.get_water_fat_shift()
PARRECHeader.set_data_offset()
PARRECImage
- exts2pars
- one_line
- parse_PAR_header
- vol_is_full
- vol_numbers
pointset
processing
pydicom_compat
quaternions
rstutils
spaces
spatialimages
- There are several ways of writing data.
- Files interface
HasDtype
HeaderDataError
HeaderTypeError
ImageDataError
SpatialFirstSlicer
SpatialHeader
SpatialHeader
SpatialHeader.__init__()
SpatialHeader.copy()
SpatialHeader.data_from_fileobj()
SpatialHeader.data_layout
SpatialHeader.data_to_fileobj()
SpatialHeader.default_x_flip
SpatialHeader.from_header()
SpatialHeader.get_base_affine()
SpatialHeader.get_best_affine()
SpatialHeader.get_data_dtype()
SpatialHeader.get_data_shape()
SpatialHeader.get_zooms()
SpatialHeader.set_data_dtype()
SpatialHeader.set_data_shape()
SpatialHeader.set_zooms()
SpatialImage
SpatialProtocol
- supported_np_types
spm2analyze
spm99analyze
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
ArraySequence
ArraySequence.__init__()
ArraySequence.append()
ArraySequence.common_shape
ArraySequence.copy()
ArraySequence.extend()
ArraySequence.finalize_append()
ArraySequence.get_data()
ArraySequence.is_array_sequence
ArraySequence.is_sliced_view
ArraySequence.load()
ArraySequence.save()
ArraySequence.shrink_data()
ArraySequence.total_nb_rows
- concatenate
- create_arraysequences_from_generator
- is_array_sequence
- is_ndarray_of_int_or_bool
Field
TckFile
LazyDict
LazyTractogram
LazyTractogram
LazyTractogram.__init__()
LazyTractogram.apply_affine()
LazyTractogram.copy()
LazyTractogram.data
LazyTractogram.data_per_point
LazyTractogram.data_per_streamline
LazyTractogram.extend()
LazyTractogram.from_data_func()
LazyTractogram.from_tractogram()
LazyTractogram.streamlines
LazyTractogram.to_world()
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
- Module:
tmpdirs
tripwire
viewers
volumeutils
wrapstruct
- wrapstruct
LabeledWrapStruct
WrapStruct
WrapStruct
WrapStruct.__init__()
WrapStruct.as_byteswapped()
WrapStruct.binaryblock
WrapStruct.check_fix()
WrapStruct.copy()
WrapStruct.default_structarr()
WrapStruct.diagnose_binaryblock()
WrapStruct.endianness
WrapStruct.from_fileobj()
WrapStruct.get()
WrapStruct.guessed_endian()
WrapStruct.items()
WrapStruct.keys()
WrapStruct.structarr
WrapStruct.template_dtype
WrapStruct.values()
WrapStruct.write_to()
WrapStructError
xmlutils