labs.mask¶
Module: labs.mask
¶
Utilities for extracting masks from EPI images and applying them to time series.
Functions¶
- nipy.labs.mask.compute_mask(mean_volume, reference_volume=None, m=0.2, M=0.9, cc=True, opening=2, exclude_zeros=False)¶
Compute a mask file from fMRI data in 3D or 4D ndarrays.
Compute and write the mask of an image based on the grey level This is based on an heuristic proposed by T.Nichols: find the least dense point of the histogram, between fractions m and M of the total image histogram.
In case of failure, it is usually advisable to increase m.
- Parameters:
- mean_volume3D ndarray
mean EPI image, used to compute the threshold for the mask.
- reference_volume: 3D ndarray, optional
reference volume used to compute the mask. If none is give, the mean volume is used.
- mfloat, optional
lower fraction of the histogram to be discarded.
- M: float, optional
upper fraction of the histogram to be discarded.
- cc: boolean, optional
if cc is True, only the largest connect component is kept.
- opening: int, optional
if opening is larger than 0, an morphological opening is performed, to keep only large structures. This step is useful to remove parts of the skull that might have been included.
- exclude_zeros: boolean, optional
Consider zeros as missing values for the computation of the threshold. This option is useful if the images have been resliced with a large padding of zeros.
- Returns:
- mask3D boolean ndarray
The brain mask
- nipy.labs.mask.compute_mask_files(input_filename, output_filename=None, return_mean=False, m=0.2, M=0.9, cc=1, exclude_zeros=False, opening=2)¶
Compute a mask file from fMRI nifti file(s)
Compute and write the mask of an image based on the grey level This is based on an heuristic proposed by T.Nichols: find the least dense point of the histogram, between fractions m and M of the total image histogram.
In case of failure, it is usually advisable to increase m.
- Parameters:
- input_filenamestring
nifti filename (4D) or list of filenames (3D).
- output_filenamestring or None, optional
path to save the output nifti image (if not None).
- return_meanboolean, optional
if True, and output_filename is None, return the mean image also, as a 3D array (2nd return argument).
- mfloat, optional
lower fraction of the histogram to be discarded.
- M: float, optional
upper fraction of the histogram to be discarded.
- cc: boolean, optional
if cc is True, only the largest connect component is kept.
- exclude_zeros: boolean, optional
Consider zeros as missing values for the computation of the threshold. This option is useful if the images have been resliced with a large padding of zeros.
- opening: int, optional
Size of the morphological opening performed as post-processing
- Returns:
- mask3D boolean array
The brain mask
- mean_image3d ndarray, optional
The main of all the images used to estimate the mask. Only provided if return_mean is True.
- nipy.labs.mask.compute_mask_sessions(session_images, m=0.2, M=0.9, cc=1, threshold=0.5, exclude_zeros=False, return_mean=False, opening=2)¶
Compute a common mask for several sessions of fMRI data.
Uses the mask-finding algorithms to extract masks for each session, and then keep only the main connected component of the a given fraction of the intersection of all the masks.
- Parameters:
- session_imageslist of (list of strings) or nipy image objects
A list of images/list of nifti filenames. Each inner list/image represents a session.
- mfloat, optional
lower fraction of the histogram to be discarded.
- M: float, optional
upper fraction of the histogram to be discarded.
- cc: boolean, optional
if cc is True, only the largest connect component is kept.
- thresholdfloat, optional
the inter-session threshold: the fraction of the total number of session in for which a voxel must be in the mask to be kept in the common mask. threshold=1 corresponds to keeping the intersection of all masks, whereas threshold=0 is the union of all masks.
- exclude_zeros: boolean, optional
Consider zeros as missing values for the computation of the threshold. This option is useful if the images have been resliced with a large padding of zeros.
- return_mean: boolean, optional
if return_mean is True, the mean image across subjects is returned.
- opening: int, optional,
size of the morphological opening
- Returns:
- mask3D boolean ndarray
The brain mask
- mean3D float array
The mean image
- nipy.labs.mask.intersect_masks(input_masks, output_filename=None, threshold=0.5, cc=True)¶
Given a list of input mask images, generate the output image which is the the threshold-level intersection of the inputs
- Parameters:
- input_masks: list of strings or ndarrays
paths of the input images nsubj set as len(input_mask_files), or individual masks.
- output_filename, string:
Path of the output image, if None no file is saved.
- threshold: float within [0, 1[, optional
gives the level of the intersection. threshold=1 corresponds to keeping the intersection of all masks, whereas threshold=0 is the union of all masks.
- cc: bool, optional
If true, extract the main connected component
- Returns:
- grp_mask, boolean array of shape the image shape
- nipy.labs.mask.largest_cc(mask)¶
Return the largest connected component of a 3D mask array.
- Parameters:
- mask: 3D boolean array
3D array indicating a mask.
- Returns:
- mask: 3D boolean array
3D array indicating a mask, with only one connected component.
- nipy.labs.mask.series_from_mask(filenames, mask, dtype=<class 'numpy.float32'>, smooth=False, ensure_finite=True)¶
Read the time series from the given sessions filenames, using the mask.
- Parameters:
- filenames: list of 3D nifti file names, or 4D nifti filename.
Files are grouped by session.
- mask: 3d ndarray
3D mask array: true where a voxel should be used.
- smooth: False or float, optional
If smooth is not False, it gives the size, in voxel of the spatial smoothing to apply to the signal.
- ensure_finite: boolean, optional
If ensure_finite is True, the non-finite values (NaNs and infs) found in the images will be replaced by zeros
- Returns:
- session_series: ndarray
3D array of time course: (session, voxel, time)
- header: header object
The header of the first file.
Notes
When using smoothing, ensure_finite should be True: as elsewhere non finite values will spread across the image.
- nipy.labs.mask.threshold_connect_components(map, threshold, copy=True)¶
- Given a map with some coefficients set to zero, segment the
connect components with number of voxels smaller than the threshold and set them to 0.
- Parameters:
- map: ndarray,
The spatial map to segment
- threshold: scalar,
The minimum number of voxels to keep a cluster.
- copy: bool, optional
If copy is false, the input array is modified inplace
- Returns:
- map: ndarray,
the map with connected components removed