nireports.interfaces package¶
NiPype interfaces to generate reportlets.
- class nireports.interfaces.CompCorVariancePlot(from_file=None, resource_monitor=None, **inputs)[source]¶
Bases:
nipype.interfaces.base.core.SimpleInterface
Plot the number of components necessary to explain the specified levels of variance.
- Mandatory Inputs
metadata_files (a list of items which are a pathlike object or string representing an existing file) – List of files containing component metadata.
- Optional Inputs
metadata_sources (a list of items which are a string) – List of names of decompositions (e.g., aCompCor, tCompCor) yielding the arguments in metadata_files.
out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value:
None
)variance_thresholds (a tuple of the form: (a float, a float, a float)) – Levels of explained variance to include in plot. (Nipype default value:
(0.5, 0.7, 0.9)
)
- Outputs
out_file (a pathlike object or string representing an existing file) – Path to saved plot.
- class nireports.interfaces.ConfoundsCorrelationPlot(from_file=None, resource_monitor=None, **inputs)[source]¶
Bases:
nipype.interfaces.base.core.SimpleInterface
Plot the correlation among confound regressors.
- Mandatory Inputs
confounds_file (a pathlike object or string representing an existing file) – File containing confound regressors.
- Optional Inputs
columns (a list of items which are a string) – Filter out all regressors not found in this list.
ignore_initial_volumes (an integer) – Number of non-steady-state volumes at the beginning of the scan to ignore. (Nipype default value:
0
)max_dim (an integer) – Maximum number of regressors to include in plot. Regressors with highest magnitude of correlation with reference_column will be selected. (Nipype default value:
20
)out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value:
None
)reference_column (a string) – Column in the confound file for which all correlation magnitudes should be ranked and plotted. (Nipype default value:
global_signal
)
- Outputs
out_file (a pathlike object or string representing an existing file) – Path to saved plot.
- class nireports.interfaces.FMRISummary(from_file=None, resource_monitor=None, **inputs)[source]¶
Bases:
nipype.interfaces.base.core.SimpleInterface
Prepare an fMRI summary plot for the report.
- Mandatory Inputs
in_func (a pathlike object or string representing an existing file)
- Optional Inputs
drop_trs (an integer) – Dummy scans. (Nipype default value:
0
)dvars (a pathlike object or string representing an existing file)
fd (a pathlike object or string representing an existing file)
fd_thres (a float) – (Nipype default value:
0.2
)in_segm (a pathlike object or string representing an existing file)
in_spikes_bg (a pathlike object or string representing an existing file)
outliers (a pathlike object or string representing an existing file)
tr (a float or None) – The TR. (Nipype default value:
None
)
- Outputs
out_file (a pathlike object or string representing an existing file) – Written file path.
- class nireports.interfaces.PlotContours(from_file=None, resource_monitor=None, **inputs)[source]¶
Bases:
nipype.interfaces.base.core.SimpleInterface
Plot contours
- Mandatory Inputs
in_contours (a pathlike object or string representing an existing file) – File to pick the contours from.
in_file (a pathlike object or string representing an existing file) – File to be plotted.
- Optional Inputs
colors (a list of items which are a string) – Colors to be used for contours. (Nipype default value:
['r']
)cut_coords (an integer) – Number of slices. (Nipype default value:
8
)display_mode (‘ortho’ or ‘x’ or ‘y’ or ‘z’ or ‘yx’ or ‘xz’ or ‘yz’) – Visualization mode. (Nipype default value:
ortho
)levels (a list of items which are a float) – Add a contour per level. (Nipype default value:
[0.5]
)out_file (a string or os.PathLike object) – Output file name.
saturate (a boolean) – Saturate background. (Nipype default value:
False
)vmax (a float) – Maximum intensity.
vmin (a float) – Minimum intensity.
- Outputs
out_file (a pathlike object or string representing an existing file) – Output svg file.
- class nireports.interfaces.PlotMosaic(from_file=None, resource_monitor=None, **inputs)[source]¶
Bases:
nipype.interfaces.base.core.SimpleInterface
Plots slices of a 3D volume into a pdf file
- Mandatory Inputs
in_file (a pathlike object or string representing an existing file) – File to be plotted.
- Optional Inputs
annotate (a boolean) – Annotate left/right. (Nipype default value:
True
)bbox_mask_file (a pathlike object or string representing an existing file) – Brain mask.
cmap (a string) – (Nipype default value:
Greys_r
)dpi (an integer) – Desired DPI of figure. (Nipype default value:
300
)figsize (a tuple of the form: (a float, a float)) – Figure size. (Nipype default value:
(11.69, 8.27)
)only_noise (a boolean) – Plot only noise. (Nipype default value:
False
)out_file (a pathlike object or string representing a file) – Output file name. (Nipype default value:
mosaic.svg
)title (a string) – A title string for the plot.
view (a list of from 1 to 3 items which are ‘axial’ or ‘sagittal’ or ‘coronal’) – (Nipype default value:
['axial', 'sagittal']
)
- Outputs
out_file (a pathlike object or string representing an existing file) – Output pdf file.
- class nireports.interfaces.PlotSpikes(from_file=None, resource_monitor=None, **inputs)[source]¶
Bases:
nipype.interfaces.base.core.SimpleInterface
Plot slices of a dataset with spikes.
- Mandatory Inputs
in_fft (a pathlike object or string representing an existing file) – Nifti file with the 4D FFT.
in_file (a pathlike object or string representing an existing file) – File to be plotted.
in_spikes (a pathlike object or string representing an existing file) – Tsv file of spikes.
- Optional Inputs
annotate (a boolean) – Annotate left/right. (Nipype default value:
True
)cmap (a string) – (Nipype default value:
Greys_r
)dpi (an integer) – Desired DPI of figure. (Nipype default value:
300
)figsize (a tuple of the form: (a float, a float)) – Figure size. (Nipype default value:
(11.69, 8.27)
)out_file (a pathlike object or string representing a file) – Output file name. (Nipype default value:
mosaic.svg
)title (a string) – A title string for the plot.
- Outputs
out_file (a pathlike object or string representing an existing file) – Output svg file.