[Mne_analysis] using SSP projections for eye blink correction and mne_process raw

[David I Leitman]

Hi All, 

Below is a snippet of code that I use: for finding EOG and ECG event and correcting for them:


###################################################
    
     print 'Implementing ECG and EOG artifact rejection on data'

    ecg_events, _, _  = mne.preprocessing.find_ecg_events(raw_in)
    if not len(ecg_events) < 20:
    
		print ecg_event_fname
		print "Writing ECG events in %s" % ecg_event_fname
		mne.write_events(ecg_event_fname, ecg_events)

		# Making projector
		print 'Computing ECG projector'

		command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
				   '--projtmin -0.08 --projtmax 0.08 --saveprojtag _ecg_proj '
				   '--projnmag 1 --projngrad 1 --projneeg 1 --projevent 999 --highpass 5 '
				   '--lowpass 35 --projmagrej 4000  --projgradrej 3000 --projeegrej 500'
				   % (in_path, in_fif_fname, ecg_event_fname))
		st = os.system(command)
		if st != 0:
			print "Error while running : %s" % command


	####################################################

    eog_events = mne.preprocessing.find_eog_events(raw_in)    
    if not len(eog_events) < 25:
    	
		print "Writing EOG events in %s" % eog_event_fname
		mne.write_events(eog_event_fname, eog_events)

		print 'Computing EOG projector'

		command = ('mne_process_raw --cd %s --raw %s --events %s --makeproj '
				   '--projtmin -0.15 --projtmax 0.15 --saveprojtag _eog_proj '
				   '--projnmag 1 --projngrad 1 --projneeg 1 --projevent 998 --lowpass 35 '
				   '--projmagrej 4000  --projgradrej 3000 --projeegrej 500' % (in_path,
				   in_fif_fname, eog_event_fname))	
		print 'Running : %s' % command	
		st = os.system(command)
		if st != 0:
			raise ValueError('Problem while running : %s' % command)
	####################################################

My question is regarding the  settings : " --projmagrej 4000  --projgradrej 3000 --projeegrej 500" what do these setting lmits mean:
 calling the help I get the following:

-projgradrej value/fT/cm rejection limit for planar gradiometers in projection calculation (default = 2000.0 fT/cm)
        --projmagrej value/fT     rejection limit magnetometers / axial gradiometers in projection calculation (default = 3000.0 fT)
        --projeegrej value/uV     rejection limit EEG in projection calculation (default = 50.0 uV)

does this mean rejecting an an eyeblink event above the listed value? If so they seem low. Given that these levels are subjecto the recording  environment/ noise, Are my limits (--projmagrej 4000  --projgradrej 3000 --projeegrej 500) good ?

For reference my rejection criteria when epoching and averaging my  data are the following :

grad= 9e-11, # T / m (gradiometers)
mag = 4.0e-12, # T (magnetometers)
eeg =150e-6, # (eeg channels)


Thanks !

Dave






David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page:	http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
 http://davidileitman.com

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