algorithms.diagnostics.screens¶
Module: algorithms.diagnostics.screens
¶
Diagnostic 4d image screen
Functions¶
- nipy.algorithms.diagnostics.screens.screen(img4d, ncomp=10, time_axis='t', slice_axis=None)¶
Diagnostic screen for 4d FMRI image
Includes PCA, tsdiffana and mean, std, min, max images.
- Parameters:
- img4d
Image
4d image file
- ncompint, optional
number of component images to return. Default is 10
- time_axisstr or int, optional
Axis over which to do PCA, time difference analysis. Defaults to t
- slice_axisNone or str or int, optional
Name or index of input axis over which to do slice analysis for time difference analysis. If None, look for input axis
slice
. At the moment we then assume slice is the last non-time axis, but this last guess we will remove in future versions of nipy. The default will then be ‘slice’ and you’ll get an error if there is no axis named ‘slice’.
- img4d
- Returns:
- screendict
with keys:
mean : mean image (all summaries are over last dimension)
std : standard deviation image
max : image of max
min : min
pca : 4D image of PCA component images
pca_res : dict of results from PCA
ts_res : dict of results from tsdiffana
Examples
>>> import nipy as ni >>> from nipy.testing import funcfile >>> img = ni.load_image(funcfile) >>> screen_res = screen(img) >>> screen_res['mean'].ndim 3 >>> screen_res['pca'].ndim 4
- nipy.algorithms.diagnostics.screens.write_screen_res(res, out_path, out_root, out_img_ext='.nii', pcnt_var_thresh=0.1)¶
Write results from
screen
to disk as images- Parameters:
- resdict
output from
screen
function- out_pathstr
directory to which to write output images
- out_rootstr
part of filename between image-specific prefix and image-specific extension to use for writing images
- out_img_extstr, optional
extension (identifying image type) to which to write volume images. Default is ‘.nii’
- pcnt_var_threshfloat, optional
threshold below which we do not plot percent variance explained by components; default is 0.1. This removes the long tail from percent variance plots.
- Returns:
- None