freesurfer

Reading functions for freesurfer files

Module: freesurfer.io

Read / write FreeSurfer geometry, morphometry, label, annotation formats

read_annot(filepath[, orig_ids])

Read in a Freesurfer annotation from a .annot file.

read_geometry(filepath[, read_metadata, ...])

Read a triangular format Freesurfer surface mesh.

read_label(filepath[, read_scalars])

Load in a Freesurfer .label file.

read_morph_data(filepath)

Read a Freesurfer morphometry data file.

write_annot(filepath, labels, ctab, names[, ...])

Write out a "new-style" Freesurfer annotation file.

write_geometry(filepath, coords, faces[, ...])

Write a triangular format Freesurfer surface mesh.

write_morph_data(file_like, values[, fnum])

Write Freesurfer morphometry data values to file-like file_like

Module: freesurfer.mghformat

Header and image reading / writing functions for MGH image format

Author: Krish Subramaniam

MGHError

Exception for MGH format related problems.

MGHHeader([binaryblock, check])

Class for MGH format header

MGHImage(dataobj, affine[, header, extra, ...])

Class for MGH format image

read_annot

nibabel.freesurfer.io.read_annot(filepath, orig_ids=False)

Read in a Freesurfer annotation from a .annot file.

An .annot file contains a sequence of vertices with a label (also known as an “annotation value”) associated with each vertex, and then a sequence of colors corresponding to each label.

Annotation file format versions 1 and 2 are supported, corresponding to the “old-style” and “new-style” color table layout.

Note that the output color table ctab is in RGBT form, where T (transparency) is 255 - alpha.

See:
Parameters:
filepathstr

Path to annotation file.

orig_idsbool

Whether to return the vertex ids as stored in the annotation file or the positional colortable ids. With orig_ids=False vertices with no id have an id set to -1.

Returns:
labelsndarray, shape (n_vertices,)

Annotation id at each vertex. If a vertex does not belong to any label and orig_ids=False, its id will be set to -1.

ctabndarray, shape (n_labels, 5)

RGBT + label id colortable array.

nameslist of bytes

The names of the labels. The length of the list is n_labels.

read_geometry

nibabel.freesurfer.io.read_geometry(filepath, read_metadata=False, read_stamp=False)

Read a triangular format Freesurfer surface mesh.

Parameters:
filepathstr

Path to surface file.

read_metadatabool, optional

If True, read and return metadata as key-value pairs.

Valid keys:

  • ‘head’ : array of int

  • ‘valid’ : str

  • ‘filename’ : str

  • ‘volume’ : array of int, shape (3,)

  • ‘voxelsize’ : array of float, shape (3,)

  • ‘xras’ : array of float, shape (3,)

  • ‘yras’ : array of float, shape (3,)

  • ‘zras’ : array of float, shape (3,)

  • ‘cras’ : array of float, shape (3,)

read_stampbool, optional

Return the comment from the file

Returns:
coordsnumpy array

nvtx x 3 array of vertex (x, y, z) coordinates.

facesnumpy array

nfaces x 3 array of defining mesh triangles.

volume_infoOrderedDict

Returned only if read_metadata is True. Key-value pairs found in the geometry file.

create_stampstr

Returned only if read_stamp is True. The comment added by the program that saved the file.

read_label

nibabel.freesurfer.io.read_label(filepath, read_scalars=False)

Load in a Freesurfer .label file.

Parameters:
filepathstr

Path to label file.

read_scalarsbool, optional

If True, read and return scalars associated with each vertex.

Returns:
label_arraynumpy array

Array with indices of vertices included in label.

scalar_arraynumpy array (floats)

Only returned if read_scalars is True. Array of scalar data for each vertex.

read_morph_data

nibabel.freesurfer.io.read_morph_data(filepath)

Read a Freesurfer morphometry data file.

This function reads in what Freesurfer internally calls “curv” file types, (e.g. ?h. curv, ?h.thickness), but as that has the potential to cause confusion where “curv” also refers to the surface curvature values, we refer to these files as “morphometry” files with PySurfer.

Parameters:
filepathstr

Path to morphometry file

Returns:
curvnumpy array

Vector representation of surface morpometry values

write_annot

nibabel.freesurfer.io.write_annot(filepath, labels, ctab, names, fill_ctab=True)

Write out a “new-style” Freesurfer annotation file.

Note that the color table ctab is in RGBT form, where T (transparency) is 255 - alpha.

See:
Parameters:
filepathstr

Path to annotation file to be written

labelsndarray, shape (n_vertices,)

Annotation id at each vertex.

ctabndarray, shape (n_labels, 5)

RGBT + label id colortable array.

nameslist of str

The names of the labels. The length of the list is n_labels.

fill_ctab{True, False} optional

If True, the annotation values for each vertex are automatically generated. In this case, the provided ctab may have shape (n_labels, 4) or (n_labels, 5) - if the latter, the final column is ignored.

write_geometry

nibabel.freesurfer.io.write_geometry(filepath, coords, faces, create_stamp=None, volume_info=None)

Write a triangular format Freesurfer surface mesh.

Parameters:
filepathstr

Path to surface file.

coordsnumpy array

nvtx x 3 array of vertex (x, y, z) coordinates.

facesnumpy array

nfaces x 3 array of defining mesh triangles.

create_stampstr, optional

User/time stamp (default: “created by <user> on <ctime>”)

volume_infodict-like or None, optional

Key-value pairs to encode at the end of the file.

Valid keys:

  • ‘head’ : array of int

  • ‘valid’ : str

  • ‘filename’ : str

  • ‘volume’ : array of int, shape (3,)

  • ‘voxelsize’ : array of float, shape (3,)

  • ‘xras’ : array of float, shape (3,)

  • ‘yras’ : array of float, shape (3,)

  • ‘zras’ : array of float, shape (3,)

  • ‘cras’ : array of float, shape (3,)

write_morph_data

nibabel.freesurfer.io.write_morph_data(file_like, values, fnum=0)

Write Freesurfer morphometry data values to file-like file_like

Equivalent to FreeSurfer’s write_curv.m

See also: http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm#CurvNew

Parameters:
file_likefile-like

String containing path of file to be written, or file-like object, open in binary write (‘wb’ mode, implementing the write method)

valuesarray-like

Surface morphometry values. Shape must be (N,), (N, 1), (1, N) or (N, 1, 1)

fnumint, optional

Number of faces in the associated surface.

MGHError

class nibabel.freesurfer.mghformat.MGHError

Bases: Exception

Exception for MGH format related problems.

To be raised whenever MGH is not happy, or we are not happy with MGH.

__init__(*args, **kwargs)

MGHHeader

class nibabel.freesurfer.mghformat.MGHHeader(binaryblock=None, check=True)

Bases: LabeledWrapStruct, SpatialHeader

Class for MGH format header

The header also consists of the footer data which MGH places after the data chunk.

Initialize header from binary data block

Parameters:
binaryblock{None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

checkbool, optional

Whether to check content of header in initialization. Default is True.

__init__(binaryblock=None, check=True)

Initialize header from binary data block

Parameters:
binaryblock{None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

checkbool, optional

Whether to check content of header in initialization. Default is True.

as_byteswapped(endianness=None)

Return new object with given endianness

If big endian, returns a copy of the object. Otherwise raises ValueError.

Parameters:
endiannessNone or string, optional

endian code to which to swap. None means swap from current endianness, and is the default

Returns:
wstrMGHHeader

MGHHeader object

static chk_version(hdr, fix=False)
copy()

Return copy of structure

data_from_fileobj(fileobj)

Read data array from fileobj

Parameters:
fileobjfile-like

Must be open, and implement read and seek methods

Returns:
arrndarray

data array

classmethod default_structarr(endianness=None)

Return header data for empty header

Ignores byte order; always big endian

classmethod diagnose_binaryblock(binaryblock, endianness=None)

Run checks over binary data, return string

classmethod from_fileobj(fileobj, check=True)

classmethod for loading a MGH fileobject

classmethod from_header(header=None, check=True)

Class method to create MGH header from another MGH header

get_affine()

Get the affine transform from the header information.

MGH format doesn’t store the transform directly. Instead it’s gleaned from the zooms ( delta ), direction cosines ( Mdc ), RAS centers ( Pxyz_c ) and the dimensions.

get_best_affine()

Get the affine transform from the header information.

MGH format doesn’t store the transform directly. Instead it’s gleaned from the zooms ( delta ), direction cosines ( Mdc ), RAS centers ( Pxyz_c ) and the dimensions.

get_data_bytespervox()

Get the number of bytes per voxel of the data

get_data_dtype()

Get numpy dtype for MGH data

For examples see set_data_dtype

get_data_offset()

Return offset into data file to read data

get_data_shape()

Get shape of data

get_data_size()

Get the number of bytes the data chunk occupies.

Return offset where the footer resides. Occurs immediately after the data chunk.

get_ras2vox()

return the inverse get_affine()

get_slope_inter()

MGH format does not do scaling?

get_vox2ras()

return the get_affine()

get_vox2ras_tkr()

Get the vox2ras-tkr transform. See “Torig” here: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

get_zooms()

Get zooms from header

Returns the spacing of voxels in the x, y, and z dimensions. For four-dimensional files, a fourth zoom is included, equal to the repetition time (TR) in ms (see The MGH/MGZ Volume Format).

To access only the spatial zooms, use hdr[‘delta’].

Returns:
ztuple

tuple of header zoom values

classmethod guessed_endian(mapping)

MGHHeader data must be big-endian

set_data_dtype(datatype)

Set numpy dtype for data from code or dtype or type

set_data_shape(shape)

Set shape of data

Parameters:
shapesequence

sequence of integers specifying data array shape

set_zooms(zooms)

Set zooms into header fields

Sets the spacing of voxels in the x, y, and z dimensions. For four-dimensional files, a temporal zoom (repetition time, or TR, in ms) may be provided as a fourth sequence element.

Parameters:
zoomssequence

sequence of floats specifying spatial and (optionally) temporal zooms

template_dtype = dtype([('version', '>i4'), ('dims', '>i4', (4,)), ('type', '>i4'), ('dof', '>i4'), ('goodRASFlag', '>i2'), ('delta', '>f4', (3,)), ('Mdc', '>f4', (3, 3)), ('Pxyz_c', '>f4', (3,)), ('tr', '>f4'), ('flip_angle', '>f4'), ('te', '>f4'), ('ti', '>f4'), ('fov', '>f4')])
writeftr_to(fileobj)

Write footer to fileobj

Footer data is located after the data chunk. So move there and write.

Parameters:
fileobjfile-like object

Should implement write and seek method

Returns:
None
writehdr_to(fileobj)

Write header to fileobj

Write starts at the beginning.

Parameters:
fileobjfile-like object

Should implement write and seek method

Returns:
None

MGHImage

class nibabel.freesurfer.mghformat.MGHImage(dataobj, affine, header=None, extra=None, file_map=None)

Bases: SpatialImage, SerializableImage

Class for MGH format image

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

affineNone or (4,4) array-like

homogeneous 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 containing image data. It should be some object that returns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogeneous 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 ArrayProxy

files_types: tuple[ExtensionSpec, ...] = (('image', '.mgh'),)
classmethod filespec_to_file_map(filespec)

Make file_map for this class from filename filespec

Class method

Parameters:
filespecstr or os.PathLike

Filename that might be for this image file type.

Returns:
file_mapdict

file_map dict with (key, value) pairs of (file_type, FileHolder instance), where file_type is a string giving the type of the contained file.

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)

Class method to create image from mapping in file_map

Parameters:
file_mapdict

Mapping with (key, value) pairs of (file_type, FileHolder instance giving file-likes for each file needed for this image type.

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_map 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.

Returns:
imgMGHImage instance
header_class

alias of MGHHeader

makeable: bool = True
rw: bool = True
to_file_map(file_map=None)

Write image to file_map or contained self.file_map

Parameters:
file_mapNone or mapping, optional

files mapping. If None (default) use object’s file_map attribute instead

valid_exts: tuple[str, ...] = ('.mgh', '.mgz')