[Mne_analysis] Making SSP files with python

Jon Houck jhouck at unm.edu
Fri Feb 17 19:08:37 EST 2012
Search archives:

Hi all,

I've been working with the python tools to build SSP projectors for EOG and
ECG.   I had thought that it might be necessary to use make_projector after
compute_spatial_vectors, but write_proj seems to work perfectly well with
the output from compute_spatial_vectors. The output files are usable in
both MNE and Neuromag.  As with projectors build using mne_process_raw,
xfit treats these projectors as if they had been applied explicitly to the
data.  Using the sample data, what I'm doing is:

raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'
raw = fiff.Raw(raw_fname)
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053']

# Make list of channel names into an array suitable for index
names = np.array(raw.info['ch_names'], dtype='S7')

# Do EOG
event_id = 998
eog_events = mne.artifacts.find_eog_events(raw, event_id)
picks = fiff.pick_types(raw.info, meg=True, eeg=False, eog=False,
ecg=False, stim=False, exclude=exclude)
ch_names = names[picks]
tmin, tmax = -0.5, 0.5
epochs = mne.Epochs(raw, eog_events, event_id, tmin, tmax,
baseline=(-0.5,-0.2), picks=picks, proj=False)
data = epochs.get_data()
EOGprojs = fiff.proj.compute_spatial_vectors(epochs, n_grad=1, n_mag=1,
n_eeg=0)

EOGprojfile =  raw_fname[:-4] + '_EOG_auto-proj.fif'
fid = fiff.write.start_file(EOGprojfile)
fiff.proj.write_proj(fid, EOGprojs)
fiff.write.end_file(fid)


Am I skipping a step somewhere along the way, or does this seem reasonable?
  I've attached the complete script, in case it's helpful.

Thanks,

Jon Houck
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20120217/1de1092a/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: make_eog_ecg_ssp.py
Type: text/x-python
Size: 3484 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20120217/1de1092a/attachment.py 


More information about the Mne_analysis mailing list