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Access a cacophony of neuro-imaging file formats
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API Reference
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nibabel
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Citing nibabel
Quickstart
get_info
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.parse_cifti2
Cifti2BrainModel
Cifti2Header
Cifti2HeaderError
Cifti2Image
Cifti2Label
Cifti2LabelTable
Cifti2Matrix
Cifti2MatrixIndicesMap
Cifti2MetaData
Cifti2NamedMap
Cifti2Parcel
Cifti2Surface
Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ
Cifti2VertexIndices
Cifti2Vertices
Cifti2Volume
Cifti2VoxelIndicesIJK
load
save
Cifti2Extension
Cifti2Parser
cmdline
Module:
cmdline.dicomfs
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
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
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
MincFile
MincHeader
MincImage
MincImageArrayProxy
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
FileNotFoundError
asbytes_nested
asunicode
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