# This sets the position of the head relative to the sensors. These values a
# A typical head position. So now in sensor space everyone is aligned. However
# We should also note that for source analysis it is better to leave this as
# the mne-fun default
params.trans_to = (0., 0., .03)
params.sss_type = 'python'
params.sss_regularize = 'svd' # 'in' by default
params.tsss_dur = 60. # 60 for adults with not much head movements. This was set to 6.
#params.st_correlation = 0.9
params.auto_bad_meg_thresh = 10 # THIS SHOULD NOT BE SO HIGH!
#Regular subjects
out,ind = nlr_organizeMEG_mnefun(raw_dir=raw_dir,out_dir=out_dir,subs=subs)
print(out)
params.subjects.sort() # Sort the subject list
print("Done sorting subjects.\n")
for n, s in enumerate(out):
print(s)
for n, s in enumerate(out):
params.subjects = [s]
params.t_adjust = -39e-3 # time delay from the trigger. It's due to set trigger function. I don't know why...
#print("Running " + str(len(params.subjects)) + ' Subjects')
params.trans_to = (0., 0., .04)
=======
params.trans_to = (0., 0., .04) # Align each subject to a common reference frame
>>>>>>> a4cd458d621a2dab85571599080677eb96297c75
params.sss_type = 'python'
params.sss_regularize = 'svd' # 'in' by default
params.tsss_dur = 10. # 60 for adults with not much head movements. This was set to 6.
params.auto_bad_meg_thresh = 30 # THIS SHOULD NOT BE SO HIGH!
# Hardcoded adult subjects here. This is temporary
#subs = glob.glob(os.path.join(raw_dir, '*mark*'))
#params.subjects = nlr_organizeMEG_mnefun(raw_dir=raw_dir,out_dir=out_dir,subs=subs)
# Regular subjects
params.subjects = nlr_organizeMEG_mnefun(raw_dir=raw_dir,out_dir=out_dir)
#params.subjects = ['112_ar150825']
params.subjects.sort() # Sort the subject list
print("Done sorting subjects.\n")
# REMOVE BAD SUBJECTS
# 101_lg150618 On entry to DLASCL parameter number 4 had an illegal value
# 103_ac150609 svd does not converge [3]: resolved!!! with tsss_dur 10
# 105_bb150713 svd does not converge: resolved!!! with tsss_dur 8
# 109_kt150814 svd does not converge: resolved!!! with tsss_dur 10
# 110_hh150824 Same as 101_lg150618: decomp_svd, DLASCL param number 4 had an illegal value
# 121_gg150904 ERROR: continuous HPI was not active in this file! [10] Only 6 sessions
# 132_wp151117: svd does not converge: resolved!!!
# 133_ml151124: svd does not converge: resolved!!!
# This sets the position of the head relative to the sensors. These values a
# A typical head position. So now in sensor space everyone is aligned. However
# We should also note that for source analysis it is better to leave this as
# the mne-fun default
params.trans_to = (0., 0., .03)
params.sss_type = 'python'
params.sss_regularize = 'svd' # 'in' by default
params.tsss_dur = 8. # 60 for adults with not much head movements. This was set to 6.
params.auto_bad_meg_thresh = 10 # THIS SHOULD NOT BE SO HIGH!
# Regular subjects
out, ind = nlr_organizeMEG_mnefun(raw_dir=raw_dir, out_dir=out_dir, subs=subs)
print(out)
#params.subjects.sort() # Sort the subject list
#print("Done sorting subjects.\n")
""" Attention!!!
"""
# REMOVE BAD SUBJECTS
badsubs = [
'103_ac150609', '105_bb150713', '108_lg150817', '109_kt150814',
'109_kt151016', '112_ar150825', '113_jk150914', '115_ps150828',
'117_cg150901', '118_ih150904', '121_gg150904', '122_jb150902',
'123_mv150918', '126_oc151026', '127_am123_md', '127_am151022',
from score import score
from nlr_organizeMEG_mnefun import nlr_organizeMEG_mnefun
out_dir = '/mnt/diskArray/scratch/NLR_MEG'
os.chdir(out_dir)
params = mnefun.Params(tmin=-0.05, tmax=1.0, t_adjust=-39e-3, n_jobs=18,
decim=2, n_jobs_mkl=1, proj_sfreq=250,
n_jobs_fir='cuda', n_jobs_resample='cuda',
filter_length='5s', epochs_type='fif', lp_cut=40.,
bmin=-0.05, auto_bad=15., plot_raw=False,
bem_type = '5120')
params.trans_to = (0., 0., .04) # Align each subject to a common reference frame
params.sss_type = 'python'
params.auto_bad_meg_thresh = 30 # THIS SHOULD NOT BE SO HIGH!
params.subjects = nlr_organizeMEG_mnefun(out_dir=out_dir)
params.subjects.sort() # Sort the subject list
# REMOVE BAD SUBJECTS
# 103_ac150609 svd does not converge [3]
# 121_gg150904 ERROR: continuous HPI was not active in this file! [10]
# 101_lg150618 SSS error [16]
# 202_dd15091 SVD does not converge [20]
# 201_gs150824 corrupted file [24]
# 201_gs150729 chpi not active [26]
# 105_bb150713 too many bad channels
# 137_gr151201 too many bad channels
# 205_ac151123 over 100 bad channels!
badsubs = ['103_ac150609','121_gg150904','101_lg150618','202_dd150919',
'201_gs150824','201_gs150729', '138_la151208', '205_ac160202', '205_ac151123']
for n, s in enumerate(badsubs):
subnum = params.subjects.index(s)
