brikhead

Class for reading AFNI BRIK/HEAD datasets

See https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html for information on what is required to have a valid BRIK/HEAD dataset.

Unless otherwise noted, descriptions AFNI attributes in the code refer to this document.

Notes

In the AFNI HEAD file, the first two values of the attribute DATASET_RANK determine the shape of the data array stored in the corresponding BRIK file. The first value, DATASET_RANK[0], must be set to 3 denoting a 3D image. The second value, DATASET_RANK[1], determines how many “sub-bricks” (in AFNI parlance) / volumes there are along the fourth (traditionally, but not exclusively) time axis. Thus, DATASET_RANK[1] will (at least as far as I (RM) am aware) always be >= 1. This permits sub-brick indexing common in AFNI programs (e.g., example4d+orig’[0]’).

AFNIArrayProxy(file_like, header[, mmap, …])

Proxy object for AFNI image array.

AFNIHeader(info)

Class for AFNI header

AFNIHeaderError

Error when reading AFNI HEAD file

AFNIImage(dataobj, affine[, header, extra, …])

AFNI Image file

AFNIImageError

Error when reading AFNI BRIK files

parse_AFNI_header(fobj)

Parses fobj to extract information from HEAD file

AFNIArrayProxy

class nibabel.brikhead.AFNIArrayProxy(file_like, header, mmap=True, keep_file_open=None)

Bases: nibabel.arrayproxy.ArrayProxy

Proxy object for AFNI image array.

Attributes
scalingnp.ndarray

Scaling factor (one factor per volume/sub-brick) for data. Default is None

Initialize AFNI array proxy

Deprecated since version 2.4.1: keep_file_open='auto' is redundant with False and has been deprecated. It will raise an error in nibabel 3.0.

Parameters
file_likefile-like object

File-like object or filename. If file-like object, should implement at least read and seek.

headerAFNIHeader object
mmap{True, False, ‘c’, ‘r’}, optional, keyword only

mmap controls the use of numpy memory mapping for reading data. If False, do not try numpy memmap for data array. If one of {‘c’, ‘r’}, try numpy memmap with mode=mmap. A mmap value of True gives the same behavior as mmap='c'. If file_like cannot be memory-mapped, ignore mmap value and read array from file.

keep_file_open{ None, True, False }, optional, keyword only

keep_file_open controls whether a new file handle is created every time the image is accessed, or a single file handle is created and used for the lifetime of this ArrayProxy. If True, a single file handle is created and used. If False, a new file handle is created every time the image is accessed. If file_like refers to an open file handle, this setting has no effect. The default value (None) will result in the value of ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` being used.

__init__(file_like, header, mmap=True, keep_file_open=None)

Initialize AFNI array proxy

Deprecated since version 2.4.1: keep_file_open='auto' is redundant with False and has been deprecated. It will raise an error in nibabel 3.0.

Parameters
file_likefile-like object

File-like object or filename. If file-like object, should implement at least read and seek.

headerAFNIHeader object
mmap{True, False, ‘c’, ‘r’}, optional, keyword only

mmap controls the use of numpy memory mapping for reading data. If False, do not try numpy memmap for data array. If one of {‘c’, ‘r’}, try numpy memmap with mode=mmap. A mmap value of True gives the same behavior as mmap='c'. If file_like cannot be memory-mapped, ignore mmap value and read array from file.

keep_file_open{ None, True, False }, optional, keyword only

keep_file_open controls whether a new file handle is created every time the image is accessed, or a single file handle is created and used for the lifetime of this ArrayProxy. If True, a single file handle is created and used. If False, a new file handle is created every time the image is accessed. If file_like refers to an open file handle, this setting has no effect. The default value (None) will result in the value of ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` being used.

scaling

AFNIHeader

class nibabel.brikhead.AFNIHeader(info)

Bases: nibabel.spatialimages.SpatialHeader

Class for AFNI header

Initialize AFNI header object

Parameters
infodict

Information from HEAD file as obtained by parse_AFNI_header()

Examples

>>> fname = os.path.join(datadir, 'example4d+orig.HEAD')
>>> header = AFNIHeader(parse_AFNI_header(fname))
>>> header.get_data_dtype().str
'<i2'
>>> header.get_zooms()
(3.0, 3.0, 3.0, 3.0)
>>> header.get_data_shape()
(33, 41, 25, 3)
__init__(info)

Initialize AFNI header object

Parameters
infodict

Information from HEAD file as obtained by parse_AFNI_header()

Examples

>>> fname = os.path.join(datadir, 'example4d+orig.HEAD')
>>> header = AFNIHeader(parse_AFNI_header(fname))
>>> header.get_data_dtype().str
'<i2'
>>> header.get_zooms()
(3.0, 3.0, 3.0, 3.0)
>>> header.get_data_shape()
(33, 41, 25, 3)
copy()

Copy object to independent representation

The copy should not be affected by any changes to the original object.

classmethod from_fileobj(fileobj)
classmethod from_header(header=None)
get_affine()

Returns affine of dataset

Examples

>>> fname = os.path.join(datadir, 'example4d+orig.HEAD')
>>> header = AFNIHeader(parse_AFNI_header(fname))
>>> header.get_affine()
array([[ -3.    ,  -0.    ,  -0.    ,  49.5   ],
       [ -0.    ,  -3.    ,  -0.    ,  82.312 ],
       [  0.    ,   0.    ,   3.    , -52.3511],
       [  0.    ,   0.    ,   0.    ,   1.    ]])
get_data_offset()

Data offset in BRIK file

Offset is always 0.

get_data_scaling()

AFNI applies volume-specific data scaling

Examples

>>> fname = os.path.join(datadir, 'scaled+tlrc.HEAD')
>>> header = AFNIHeader(parse_AFNI_header(fname))
>>> header.get_data_scaling()
array([  3.88336300e-08])
get_slope_inter()

Use self.get_data_scaling() instead

Holdover because AFNIArrayProxy (inheriting from ArrayProxy) requires this functionality so as to not error.

get_space()

Return label for anatomical space to which this dataset is aligned.

Returns
spacestr

AFNI “space” designation; one of [ORIG, ANAT, TLRC, MNI]

Notes

There appears to be documentation for these spaces at https://afni.nimh.nih.gov/pub/dist/atlases/elsedemo/AFNI_atlas_spaces.niml

get_volume_labels()

Returns volume labels

Returns
labelslist of str

Labels for volumes along fourth dimension

Examples

>>> header = AFNIHeader(parse_AFNI_header(os.path.join(datadir, 'example4d+orig.HEAD')))
>>> header.get_volume_labels()
['#0', '#1', '#2']

AFNIHeaderError

class nibabel.brikhead.AFNIHeaderError

Bases: nibabel.spatialimages.HeaderDataError

Error when reading AFNI HEAD file

__init__($self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

AFNIImage

class nibabel.brikhead.AFNIImage(dataobj, affine, header=None, extra=None, file_map=None)

Bases: nibabel.spatialimages.SpatialImage

AFNI Image file

Can be loaded from either the BRIK or HEAD file (but MUST specify one!)

Examples

>>> import nibabel as nib
>>> brik = nib.load(os.path.join(datadir, 'example4d+orig.BRIK.gz'))
>>> brik.shape
(33, 41, 25, 3)
>>> brik.affine
array([[ -3.    ,  -0.    ,  -0.    ,  49.5   ],
       [ -0.    ,  -3.    ,  -0.    ,  82.312 ],
       [  0.    ,   0.    ,   3.    , -52.3511],
       [  0.    ,   0.    ,   0.    ,   1.    ]])
>>> head = load(os.path.join(datadir, 'example4d+orig.HEAD'))
>>> np.array_equal(head.get_data(), brik.get_data())
True

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters
dataobjobject

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

__init__(dataobj, affine, header=None, extra=None, file_map=None)

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters
dataobjobject

Object containg image data. It should be some object that retuns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogenous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case, obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

ImageArrayProxy

alias of AFNIArrayProxy

files_types = (('image', '.brik'), ('header', '.head'))
classmethod filespec_to_file_map(filespec)

Make file_map from filename filespec

AFNI BRIK files can be compressed, but HEAD files cannot - see afni.nimh.nih.gov/pub/dist/doc/program_help/README.compression.html. Thus, if you have AFNI files my_image.HEAD and my_image.BRIK.gz and you want to load the AFNI BRIK / HEAD pair, you can specify:

  • The HEAD filename - e.g., my_image.HEAD

  • The BRIK filename w/o compressed extension - e.g., my_image.BRIK

  • The full BRIK filename - e.g., my_image.BRIK.gz

Parameters
filespecstr

Filename that might be for this image file type.

Returns
file_mapdict

dict with keys image and header where values are fileholder objects for the respective BRIK and HEAD files

Raises
ImageFileError

If filespec is not recognizable as being a filename for this image type.

classmethod from_file_map(file_map, mmap=True, keep_file_open=None)

Creates an AFNIImage instance from file_map

Deprecated since version 2.4.1: keep_file_open='auto' is redundant with False and has been deprecated. It will raise an error in nibabel 3.0.

Parameters
file_mapdict

dict with keys image, header and values being fileholder objects for the respective BRIK and HEAD files

mmap{True, False, ‘c’, ‘r’}, optional, keyword only

mmap controls the use of numpy memory mapping for reading image array data. If False, do not try numpy memmap for data array. If one of {‘c’, ‘r’}, try numpy memmap with mode=mmap. A mmap value of True gives the same behavior as mmap='c'. If image data file cannot be memory-mapped, ignore mmap value and read array from file.

keep_file_open{None, True, False}, optional, keyword only

keep_file_open controls whether a new file handle is created every time the image is accessed, or a single file handle is created and used for the lifetime of this ArrayProxy. If True, a single file handle is created and used. If False, a new file handle is created every time the image is accessed. If file_like refers to an open file handle, this setting has no effect. The default value (None) will result in the value of ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` being used.

header_class

alias of AFNIHeader

makeable = False
rw = False
valid_exts = ('.brik', '.head')

AFNIImageError

class nibabel.brikhead.AFNIImageError

Bases: nibabel.spatialimages.ImageDataError

Error when reading AFNI BRIK files

__init__($self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

parse_AFNI_header

nibabel.brikhead.parse_AFNI_header(fobj)

Parses fobj to extract information from HEAD file

Parameters
fobjfile-like object

AFNI HEAD file object or filename. If file object, should implement at least read

Returns
infodict

Dictionary containing AFNI-style key:value pairs from HEAD file

Examples

>>> fname = os.path.join(datadir, 'example4d+orig.HEAD')
>>> info = parse_AFNI_header(fname)
>>> print(info['BYTEORDER_STRING'])
LSB_FIRST
>>> print(info['BRICK_TYPES'])
[1, 1, 1]