eelbrain.pipeline.MneExperiment¶
-
class
eelbrain.pipeline.
MneExperiment
(root=None, find_subjects=True, **state)¶ Analyze an MEG experiment (gradiometer only) with MNE
Parameters: - root : str | None
the root directory for the experiment (usually the directory containing the ‘meg’ and ‘mri’ directories). The experiment can be initialized without the root for testing purposes.
- find_subjects : bool
Automatically look for subjects in the MEG-directory (default True). Set
find_subjects=False
to initialize the experiment without any files.- …
Initial state parameters.
Notes
See also
Guide on using The MneExperiment Pipeline.
Methods¶
clear_cache (self[, level]) |
Remove cached files. |
copy (self, temp[, dst_root, inclusive, …]) |
Copy files to a different root folder |
expand_template (self, temp[, keep]) |
Expand all constant variables in a template |
find_keys (self, temp[, root]) |
Find all terminal field names that are relevant for a template. |
format (self, string[, vmatch]) |
Format a string (i.e., replace any ‘{xxx}’ fields with their values) |
get (self, temp[, fmatch, vmatch, match, …]) |
Retrieve a formatted template |
get_field_values (self, field[, exclude]) |
Find values for a field taking into account exclusion |
glob (self, temp[, inclusive]) |
Find all files matching a certain pattern |
iter (self[, fields, exclude, values, group, …]) |
Cycle the experiment’s state through all values on the given fields |
iter_range (self[, start, stop, field]) |
Iterate through a range on a field with ordered values. |
iter_temp (self, temp[, exclude, values]) |
Iterate through all paths conforming to a template given in temp . |
label_events (self, ds) |
Add event labels to events loaded from raw files |
label_groups (self, subject, groups) |
Generate Factor for group membership |
label_subjects (self, ds) |
Label the subjects in ds |
load_annot (self, **state) |
Load a parcellation (from an annot file) |
load_bad_channels (self, **kwargs) |
Load bad channels |
load_cov (self, **kwargs) |
Load the covariance matrix |
load_edf (self, **kwargs) |
Load the edf file (“edf-file” template) |
load_epochs (self[, subjects, baseline, …]) |
Load a Dataset with epochs for a given epoch definition |
load_epochs_stc (self[, subjects, baseline, …]) |
Load a Dataset with stcs for single epochs |
load_epochs_stf (self[, subjects, baseline, …]) |
Load frequency space single trial data |
load_events (self[, subject, add_bads, data_raw]) |
Load events from a raw file. |
load_evoked (self[, subjects, baseline, …]) |
Load a Dataset with the evoked responses for each subject. |
load_evoked_stc (self[, subjects, baseline, …]) |
Load evoked source estimates. |
load_evoked_stf (self[, subjects, baseline, …]) |
Load frequency space evoked data |
load_fwd (self[, surf_ori, ndvar, mask]) |
Load the forward solution |
load_ica (self[, make]) |
Load the mne-python ICA object |
load_induced_stc (self[, subjects, …]) |
Morlet wavelet induced power and phase in source space. |
load_inv (self[, fiff, ndvar, mask]) |
Load the inverse operator |
load_label (self, label, **kwargs) |
Retrieve a label as mne Label object |
load_morph_matrix (self, **state) |
Load the morph matrix from mrisubject to common_brain |
load_neighbor_correlation (self[, subjects, …]) |
Load sensor neighbor correlation |
load_raw (self[, add_bads, preload, ndvar, decim]) |
Load a raw file as mne Raw object. |
load_selected_events (self[, subjects, …]) |
Load events and return a subset based on epoch and rejection |
load_src (self[, add_geom, ndvar]) |
Load the current source space |
load_test (self, test[, tstart, tstop, pmin, …]) |
Create and load spatio-temporal cluster test results |
make_annot (self, **state) |
Make sure the annot files for both hemispheres exist |
make_bad_channels (self[, bad_chs, redo]) |
Write the bad channel definition file for a raw file |
make_bad_channels_auto (self[, flat, redo]) |
Automatically detect bad channels |
make_bad_channels_neighbor_correlation (self, r) |
Exclude bad channels based on low average neighbor-correlation |
make_besa_evt (self[, redo]) |
Make the trigger and event files needed for besa |
make_copy (self, temp, field, src, dst[, redo]) |
Make a copy of a file to a new path by substituting one field value |
make_cov (self) |
Make a noise covariance (cov) file |
make_epoch_selection (self[, decim, auto, …]) |
Open gui.select_epochs() for manual epoch selection |
make_fwd (self) |
Make the forward model |
make_ica (self[, make]) |
Compute ICA decomposition for a pipeline.RawICA preprocessing step |
make_ica_selection (self[, epoch, decim, session]) |
Select ICA components to remove through a GUI |
make_link (self, temp, field, src, dst[, redo]) |
Make a hard link |
make_mov_ga_dspm (self[, subjects, baseline, …]) |
Make a grand average movie from dSPM values (requires PySurfer 0.6) |
make_mov_ttest (self[, subjects, model, c1, …]) |
Make a t-test movie (requires PySurfer 0.6) |
make_mrat_evoked (self, **kwargs) |
Produce the sensor data fiff files needed for MRAT sensor analysis |
make_mrat_stcs (self, **kwargs) |
Produce the STC files needed for the MRAT analysis tool |
make_plot_annot (self[, surf, redo]) |
Create a figure for the contents of an annotation file |
make_plot_label (self, label[, surf, redo]) |
|
make_plots_labels (self[, surf, redo]) |
|
make_raw (self, **kwargs) |
Make a raw file |
make_report (self, test[, parc, mask, pmin, …]) |
Create an HTML report on spatio-temporal clusters |
make_report_coreg (self[, file_name]) |
Create HTML report with plots of the MEG/MRI coregistration |
make_report_rois (self, test[, parc, pmin, …]) |
Create an HTML report on ROI time courses |
make_src (self, **kwargs) |
Make the source space |
merge_bad_channels (self) |
Merge bad channel definitions for different sessions |
move (self, temp[, dst_root, inclusive, …]) |
Move files to a different root folder |
next (self[, field]) |
Change field to the next value |
plot_annot (self[, parc, surf, views, hemi, …]) |
Plot the annot file on which the current parcellation is based |
plot_brain (self[, common_brain]) |
Plot the brain model |
plot_coreg (self[, dig, parallel]) |
Plot the coregistration (Head shape and MEG helmet) |
plot_evoked (self[, subjects, separate, …]) |
Plot evoked sensor data |
plot_label (self, label[, surf, views, w]) |
Plot a label |
plot_raw (self[, decim, xlim, add_bads, …]) |
Plot raw sensor data |
plot_whitened_gfp (self[, s_start, s_stop, run]) |
Plot the GFP of the whitened evoked to evaluate the the covariance matrix |
rename (self, old, new[, exclude]) |
Rename all files corresponding to a pattern (or template) |
rename_field (self, temp, field, old, new[, …]) |
Change the value of one field in paths corresponding to a template |
reset (self) |
Reset all field values to the state at initialization |
rm (self, temp[, inclusive, confirm]) |
Remove all files corresponding to a template |
run_mne_analyze (self[, modal]) |
Run mne_analyze |
run_mne_browse_raw (self[, modal]) |
Run mne_analyze |
set (self[, subject, match, allow_asterisk]) |
Set variable values. |
set_inv (self[, ori, snr, method, depth, …]) |
Set the type of inverse solution used for source estimation |
show_bad_channels (self[, sessions]) |
List bad channels |
show_fields (self[, str_out]) |
Generate a table for all iterable fields and ther values. |
show_file_status (self, temp[, col, row]) |
Compile a table about the existence of files |
show_file_status_mult (self, files, fields[, …]) |
Compile a table about the existence of multiple files |
show_in_finder (self, temp, **kwargs) |
Reveal the file corresponding to the temp template in the Finder. |
show_input_tree (self) |
Print a tree of the files needed as input |
show_raw_info (self, **state) |
Display the selected pipeline for raw processing |
show_reg_params (self[, asds]) |
Show the covariance matrix regularization parameters |
show_rej_info (self[, flagp, asds, bads]) |
Information about artifact rejection |
show_state (self[, temp, empty, hide]) |
List all top-level fields and their values |
show_subjects (self[, mri, mrisubject, …]) |
Create a Dataset with subject information |
show_tree (self[, root, fields]) |
Print a tree of the filehierarchy implicit in the templates |