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.. _mne_report_tutorial:
===================================
Getting started with MNE web report
===================================
This quick start will show you how to run the `mne report` command on the
sample data set provided with MNE.
First ensure that the files you want to render follow the filename conventions
defined by MNE:
================== ====================================================
Data object Filename convention (ends with)
================== ====================================================
raw -raw.fif(.gz), -raw_sss.fif(.gz), -raw_tsss.fif(.gz)
events -eve.fif(.gz)
epochs -epo.fif(.gz)
evoked -ave.fif(.gz)
covariance -cov.fif(.gz)
trans -trans.fif(.gz)
forward -fwd.fif(.gz)
inverse -inv.fif(.gz)
================== ====================================================
The command line interface
--------------------------
To generate a barebones report from all the \*.fif files in the sample dataset,
invoke the following command in a system (e.g., Bash) shell:
.. code-block:: console
$ mne report --path MNE-sample-data/ --verbose
On successful creation of the report, it will open the html in a new tab in the browser.
To disable this, use the `--no-browser` option.
If the report is generated for a single subject, give the ``SUBJECT`` name and the
``SUBJECTS_DIR`` and this will generate the MRI slices (with BEM contours overlaid on top
if available):
.. code-block:: console
$ mne report --path MNE-sample-data/ --subject sample --subjects-dir MNE-sample-data/subjects --verbose
To properly render `trans` and `covariance` files, add the measurement information:
.. code-block:: console
$ mne report --path MNE-sample-data/ --info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--subject sample --subjects-dir MNE-sample-data/subjects --verbose
To render whitened `evoked` files with baseline correction, add the noise covariance file:
.. code-block:: console
$ mne report --path MNE-sample-data/ --info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--cov MNE-sample-data/MEG/sample/sample_audvis-cov.fif --bmax 0 --subject sample \
--subjects-dir MNE-sample-data/subjects --verbose
To generate the report in parallel:
.. code-block:: console
$ mne report --path MNE-sample-data/ --info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--subject sample --subjects-dir MNE-sample-data/subjects --verbose --jobs 6
The report rendered on sample-data is shown below:
.. image:: mne-report.png
:align: center
For help on all the available options, do:
.. code-block:: console
$ mne report --help
The Python interface
--------------------
The same functionality can also be achieved using the Python interface. Import
the required functions::
>>> from mne.report import Report
>>> from mne.datasets import sample
Generate the report::
>>> path = sample.data_path(verbose=False)
>>> fname_evoked = path + '/MEG/sample/sample_audvis-ave.fif'
>>> report = Report(fname_evoked, verbose=True)
Embedding : jquery-1.10.2.min.js
Embedding : jquery-ui.min.js
Embedding : bootstrap.min.js
Embedding : jquery-ui.min.css
Embedding : bootstrap.min.css
Only include \*audvis_raw.fif and \*-eve.fif files in the report
(and decimate the MRI a lot because we don't need it)::
>>> report.parse_folder(data_path=path, pattern=['*audvis_raw.fif', '*-eve.fif'], render_bem=False) # doctest:+ELLIPSIS
Iterating over 6 potential files (this may take some time)
Rendering : .../MNE-sample-data/MEG/sample/sample_audvis_raw.fif
Opening raw data file .../MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 25800 ... 192599 = 42.956 ... 320.670 secs
Ready.
Current compensation grade : 0
Rendering : .../MNE-sample-data/MEG/sample/ernoise_raw-eve.fif
Rendering : .../MNE-sample-data/MEG/sample/sample_audvis_ecg-eve.fif
Rendering : .../MNE-sample-data/MEG/sample/sample_audvis_eog-eve.fif
Rendering : .../MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif
Rendering : .../MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif
Save the report as an html, but do not open the html in a browser::
>>> report.save('report.html', overwrite=True, open_browser=False) # doctest:+SKIP
Rendering : Table of Contents...
There is greater flexibility compared to the command line interface.
Custom plots can be added to the report. Let us first generate a custom plot::
>>> from mne import read_evokeds
>>> evoked = read_evokeds(fname_evoked, condition='Left Auditory', baseline=(None, 0), verbose=True) # doctest: +ELLIPSIS
Reading ...
Read a total of 4 projection items:
PCA-v1 (1 x 102) active
PCA-v2 (1 x 102) active
PCA-v3 (1 x 102) active
Average EEG reference (1 x 60) active
Found the data of interest:
t = -199.80 ... 499.49 ms (Left Auditory)
0 CTF compensation matrices available
nave = 55 - aspect type = 100
Projections have already been applied. Setting proj attribute to True.
Applying baseline correction (mode: mean)
>>> fig = evoked.plot(show=False, time_unit='s')
To add the custom plot to the report, do::
>>> report.add_figs_to_section(fig, captions='Left Auditory', section='evoked')
>>> report.save('report.html', overwrite=True) # doctest: +SKIP
Rendering : Table of Contents...
The MNE report command internally manages the sections so that plots belonging to the same section
are rendered consecutively. Within a section, the plots are ordered in the same order that they were
added using the `add_figs_to_section` command. Each section is identified by a toggle button in the navigation
bar of the report which can be used to show or hide the contents of the section.
Saving to HTML is a write-only operation, meaning that we cannot read an
``.html`` file back as a :class:`mne.Report` object. In order to be able to
read it back, we can save it as an HDF5 file::
>>> from mne import open_report
>>> report.save('report.h5', overwrite=True) # doctest: +SKIP
>>> open_report('report.h5') # doctest: +SKIP
This allows us to have multiple scripts that add figures to the same report. To
make this even easier, :class:`mne.Report` can be used as a context manager,
allowing you to do this::
>>> with open_report('report.h5') as report: # Creates a new report if 'report.h5' doesn't exist # doctest: +SKIP
>>> report.add_figs_to_section(fig, captions='Left Auditory', section='evoked', replace=True) # doctest: +SKIP
>>> report.save('report.html', overwrite=True) # Update the HTML page # doctest: +SKIP
>>> # Updated report is automatically saved back to 'report.h5' upon leaving the block
That's it!
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