API ReferenceΒΆ
nibabelaffinesanalyze- The Analyze header format
AnalyzeHeaderAnalyzeHeaderAnalyzeHeader.__init__()AnalyzeHeader.as_analyze_map()AnalyzeHeader.data_from_fileobj()AnalyzeHeader.data_to_fileobj()AnalyzeHeader.default_structarr()AnalyzeHeader.default_x_flipAnalyzeHeader.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_interceptAnalyzeHeader.has_data_slopeAnalyzeHeader.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_hdrAnalyzeHeader.template_dtype
AnalyzeImage
arrayproxyarraywritersbatteryrunnersbenchmarksbrikheadcaretcastingcifti2- Module:
cifti2.cifti2 - Module:
cifti2.cifti2_axes - Module:
cifti2.parse_cifti2Cifti2BrainModelCifti2HeaderCifti2HeaderErrorCifti2ImageCifti2ImageCifti2Image.__init__()Cifti2Image.files_typesCifti2Image.from_file_map()Cifti2Image.from_image()Cifti2Image.get_data_dtype()Cifti2Image.header_classCifti2Image.makeableCifti2Image.nifti_headerCifti2Image.rwCifti2Image.set_data_dtype()Cifti2Image.to_file_map()Cifti2Image.update_headers()Cifti2Image.valid_exts
Cifti2LabelCifti2LabelTableCifti2MatrixCifti2MatrixIndicesMapCifti2MetaDataCifti2NamedMapCifti2ParcelCifti2SurfaceCifti2TransformationMatrixVoxelIndicesIJKtoXYZCifti2VertexIndicesCifti2VerticesCifti2VolumeCifti2VoxelIndicesIJKLimitedNifti2HeaderAxisBrainModelAxisBrainModelAxisBrainModelAxis.__init__()BrainModelAxis.affineBrainModelAxis.from_index_mapping()BrainModelAxis.from_mask()BrainModelAxis.from_surface()BrainModelAxis.get_element()BrainModelAxis.iter_structures()BrainModelAxis.nameBrainModelAxis.surface_maskBrainModelAxis.to_cifti_brain_structure_name()BrainModelAxis.to_mapping()BrainModelAxis.volume_maskBrainModelAxis.volume_shape
LabelAxisParcelsAxisScalarAxisSeriesAxis- from_index_mapping
- to_header
Cifti2ExtensionCifti2Parser
- 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
DICOMFSFileHandledummy_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:
datadataobj_imagesdeprecateddeprecatordftecatEcatHeaderEcatImageEcatImageEcatImage.__init__()EcatImage.ImageArrayProxyEcatImage.affineEcatImage.files_typesEcatImage.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_classEcatImage.load()EcatImage.shapeEcatImage.to_file_map()EcatImage.valid_exts
EcatImageArrayProxyEcatSubHeader- get_frame_order
- get_series_framenumbers
- read_mlist
- read_subheaders
environmenteuleranglesfilebasedimagesFileBasedHeaderFileBasedImageFileBasedImageFileBasedImage.__init__()FileBasedImage.files_typesFileBasedImage.filespec_to_file_map()FileBasedImage.from_file_map()FileBasedImage.from_filename()FileBasedImage.from_image()FileBasedImage.get_filename()FileBasedImage.headerFileBasedImage.header_classFileBasedImage.instance_to_filename()FileBasedImage.load()FileBasedImage.make_file_map()FileBasedImage.makeableFileBasedImage.path_maybe_image()FileBasedImage.rwFileBasedImage.set_filename()FileBasedImage.to_file_map()FileBasedImage.to_filename()FileBasedImage.valid_exts
ImageFileErrorSerializableImage
fileholdersfilename_parserfileslicefileutilsfreesurfer- Module:
freesurfer.io - Module:
freesurfer.mghformat- read_annot
- read_geometry
- read_label
- read_morph_data
- write_annot
- write_geometry
- write_morph_data
MGHErrorMGHHeaderMGHHeaderMGHHeader.__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_dtypeMGHHeader.writeftr_to()MGHHeader.writehdr_to()
MGHImage
- Module:
funcsgifti- Module:
gifti.gifti - Module:
gifti.parse_gifti_fast - Module:
gifti.utilGiftiCoordSystemGiftiDataArrayGiftiImageGiftiImageGiftiImage.__init__()GiftiImage.add_gifti_data_array()GiftiImage.agg_data()GiftiImage.files_typesGiftiImage.from_file_map()GiftiImage.from_filename()GiftiImage.get_arrays_from_intent()GiftiImage.labeltableGiftiImage.metaGiftiImage.numDAGiftiImage.parserGiftiImage.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
GiftiLabelGiftiLabelTableGiftiMetaDataGiftiNVPairsGiftiImageParserGiftiParseError- read_data_block
- Module:
imageclassesimageglobalsimagestatsloadsaveminc1minc2mriutilsnicom- Module:
nicom.ascconv - Module:
nicom.csareader - Module:
nicom.dicomreaders - Module:
nicom.dicomwrappers - Module:
nicom.dwiparams - Module:
nicom.structreader - Module:
nicom.utilsAscconvParseErrorAtomNoValue- assign2atoms
- obj_from_atoms
- parse_ascconv
CSAErrorCSAReadError- 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
MosaicWrapperMultiframeWrapperSiemensWrapperWrapperWrapperWrapper.__init__()Wrapper.affineWrapper.b_matrixWrapper.b_value()Wrapper.b_vector()Wrapper.get()Wrapper.get_data()Wrapper.get_pixel_array()Wrapper.image_orient_patient()Wrapper.image_position()Wrapper.image_shape()Wrapper.instance_number()Wrapper.is_csaWrapper.is_mosaicWrapper.is_multiframeWrapper.is_same_series()Wrapper.q_vectorWrapper.rotation_matrix()Wrapper.series_signature()Wrapper.slice_indicator()Wrapper.slice_normal()Wrapper.voxel_sizes()
WrapperErrorWrapperPrecisionError- none_or_close
- wrapper_from_data
- wrapper_from_file
- B2q
- nearest_pos_semi_def
- q2bg
Unpacker- find_private_section
- Module:
nifti1Nifti1DicomExtensionNifti1ExtensionNifti1ExtensionsNifti1HeaderNifti1HeaderNifti1Header.__init__()Nifti1Header.copy()Nifti1Header.default_structarr()Nifti1Header.exts_klassNifti1Header.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_interceptNifti1Header.has_data_slopeNifti1Header.is_singleNifti1Header.may_contain_header()Nifti1Header.pair_magicNifti1Header.pair_vox_offsetNifti1Header.quaternion_thresholdNifti1Header.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_magicNifti1Header.single_vox_offsetNifti1Header.template_dtypeNifti1Header.write_to()
Nifti1ImageNifti1PairNifti1PairHeader- load
- save
nifti2Nifti2HeaderNifti2HeaderNifti2Header.__init__()Nifti2Header.default_structarr()Nifti2Header.get_data_shape()Nifti2Header.may_contain_header()Nifti2Header.pair_magicNifti2Header.pair_vox_offsetNifti2Header.quaternion_thresholdNifti2Header.set_data_shape()Nifti2Header.single_magicNifti2Header.single_vox_offsetNifti2Header.sizeof_hdrNifti2Header.template_dtype
Nifti2ImageNifti2PairNifti2PairHeader- load
- save
onetimeopenersDeterministicGzipFileImageOpenerOpenerOpenerOpener.__init__()Opener.bz2_defOpener.close()Opener.close_if_mine()Opener.closedOpener.compress_ext_icaseOpener.compress_ext_mapOpener.default_compresslevelOpener.default_level_or_optionOpener.default_zst_compresslevelOpener.fileno()Opener.gz_defOpener.modeOpener.nameOpener.read()Opener.readinto()Opener.seek()Opener.tell()Opener.write()Opener.zstd_def
optpkgorientationsparrec- PAR file format
PARRECArrayProxyPARRECErrorPARRECHeaderPARRECHeaderPARRECHeader.__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
processingpydicom_compatquaternionsrstutilsspacesspatialimages- There are several ways of writing data.
- Files interface
HeaderDataErrorHeaderTypeErrorImageDataErrorSpatialFirstSlicerSpatialHeaderSpatialHeaderSpatialHeader.__init__()SpatialHeader.copy()SpatialHeader.data_from_fileobj()SpatialHeader.data_layoutSpatialHeader.data_to_fileobj()SpatialHeader.default_x_flipSpatialHeader.from_fileobj()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()SpatialHeader.write_to()
SpatialImage- supported_np_types
spm2analyzespm99analyzestreamlines- 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
ArraySequenceArraySequenceArraySequence.__init__()ArraySequence.append()ArraySequence.common_shapeArraySequence.copy()ArraySequence.extend()ArraySequence.finalize_append()ArraySequence.get_data()ArraySequence.is_array_sequenceArraySequence.is_sliced_viewArraySequence.load()ArraySequence.save()ArraySequence.shrink_data()ArraySequence.total_nb_rows
- concatenate
- create_arraysequences_from_generator
- is_array_sequence
- is_ndarray_of_int_or_bool
FieldTckFileLazyDictLazyTractogramLazyTractogramLazyTractogram.__init__()LazyTractogram.apply_affine()LazyTractogram.copy()LazyTractogram.dataLazyTractogram.data_per_pointLazyTractogram.data_per_streamlineLazyTractogram.extend()LazyTractogram.from_data_func()LazyTractogram.from_tractogram()LazyTractogram.streamlinesLazyTractogram.to_world()
PerArrayDictPerArraySequenceDictSliceableDataDictTractogramTractogramItem- is_data_dict
- is_lazy_dict
DataErrorDataWarningExtensionWarningHeaderErrorHeaderWarningTractogramFileabstractclassmethodTrkFile- 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:
tmpdirstripwireviewersvolumeutilswrapstruct- wrapstruct
LabeledWrapStructWrapStructWrapStructWrapStruct.__init__()WrapStruct.as_byteswapped()WrapStruct.binaryblockWrapStruct.check_fix()WrapStruct.copy()WrapStruct.default_structarr()WrapStruct.diagnose_binaryblock()WrapStruct.endiannessWrapStruct.from_fileobj()WrapStruct.get()WrapStruct.guessed_endian()WrapStruct.items()WrapStruct.keys()WrapStruct.structarrWrapStruct.template_dtypeWrapStruct.values()WrapStruct.write_to()
WrapStructError
xmlutils