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f2f_params.yml
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f2f_params.yml
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# Analysis parameters for processing pipeline in F2F_MNEFun_Main.ipynb #
general:
subjects_dir: null
subject_indices: null
fetch_raw:
subjects: ['f2f_107']
structurals: ['f2f_107']
dates: null
acq_ssh: localhost
acq_dir: /mnt/brainstudio/mmf/
run_names: ['%s']
runs_empty: ['%s_erm']
subject_run_indices: null
scoring:
score: null
list_dir: lists_1sec
preprocessing:
multithreading:
n_jobs: 1
n_jobs_fir: 1
n_jobs_resample: 1
bads:
mf_prebad: {
__default__: [], # ERM in some 1st and 2nd lines below
f2f_009: ['MEG0313', 'MEG1023', 'MEG1043',
'MEG1321', 'MEG1442'],
f2f_010: ['MEG2113', 'MEG0733',
'MEG0422', 'MEG1321', 'MEG1442'],
f2f_011: ['MEG2113',
'MEG0142', 'MEG0422', 'MEG1321', 'MEG1442'],
f2f_012: ['MEG0422', 'MEG0933', 'MEG1321', 'MEG1521'],
f2f_013: ['MEG0733',
'MEG0142', 'MEG0422', 'MEG1442', 'MEG1321', 'MEG1521'],
f2f_014: ['MEG0142', 'MEG0422', 'MEG1321', 'MEG1442', 'MEG1522'],
f2f_015: ['MEG0142', 'MEG0422', 'MEG0331', 'MEG0933', 'MEG1442',
'MEG1321', 'MEG1521'],
f2f_018: ['MEG0413', 'MEG0422', 'MEG1442', 'MEG1321', 'MEG1521'],
f2f_021: ['MEG1113', 'MEG2113', 'MEG1321', 'MEG1521',
'MEG0413', 'MEG0422', 'MEG1442', 'MEG1842'],
f2f_022: ['MEG0733', 'MEG0933', 'MEG1321', 'MEG1521'],
f2f_024: ['MEG0422', 'MEG2613', 'MEG1321', 'MEG1521'],
f2f_025: ['MEG1543',
'MEG0142', 'MEG1523', 'MEG1321', 'MEG1521', 'MEG2121'],
f2f_025: ['MEG0422', 'MEG1442', 'MEG1321', 'MEG1521'],
f2f_027: ['MEG1523', 'MEG0142', 'MEG0422',
'MEG1321', 'MEG1521', 'MEG2121', 'MEG2441', 'MEG2611'],
f2f_028: ['MEG0331', 'MEG1523', 'MEG2611',
'MEG0142', 'MEG0422', 'MEG1321', 'MEG1521', 'MEG2121'],
f2f_029: ['MEG0142', 'MEG0413', 'MEG0422', 'MEG0933',
'MEG1321', 'MEG1521'],
f2f_030: ['MEG0413', 'MEG0422', 'MEG0743', 'MEG0933', 'MEG2532',
'MEG1321', 'MEG1521'],
f2f_034: ['MEG1223',
'MEG0422', 'MEG0743', 'MEG1442', 'MEG1321', 'MEG1521'],
f2f_036: ['MEG0713',
'MEG0422', 'MEG0743', 'MEG1442', 'MEG1321'],
f2f_037: ['MEG0422',
'MEG0142', 'MEG0743', 'MEG0933', 'MEG1442', 'MEG0611',
'MEG1321', 'MEG1521'],
f2f_038: ['MEG1432',
'MEG0142', 'MEG0422', 'MEG0743', 'MEG1442', 'MEG1321'],
f2f_041: [],
f2f_102: ['MEG1743', 'MEG2542',
'MEG0142', 'MEG0743', 'MEG1321', 'MEG1521'],
f2f_103: ['MEG0413', 'MEG1823', 'MEG1743',
'MEG0142', 'MEG0933', 'MEG2542', 'MEG1321', 'MEG1521'],
f2f_104: ['MEG1743', 'MEG2542',
'MEG0933', 'MEG1413', 'MEG1442', 'MEG1111',
'MEG1321', 'MEG1521'],
f2f_106: ['MEG1743', 'MEG1831',
'MEG0142', 'MEG0743', 'MEG2542', 'MEG1321', 'MEG1521'],
f2f_107: ['MEG0332', 'MEG1743', 'MEG2542',
'MEG0142', 'MEG0743', 'MEG0933', 'MEG1321', 'MEG1521'],
f2f_108: ['MEG1521', 'MEG1743', 'MEG2542',
'MEG0142', 'MEG0743', 'MEG1543', 'MEG2633',
'MEG1321', 'MEG1521'],
f2f_111: ['MEG1743',
'MEG0743', 'MEG2542', 'MEG1321'],
f2f_112: ['MEG1743',
'MEG0743', 'MEG1112', 'MEG1422', 'MEG2113',
'MEG2133', 'MEG2343', 'MEG2542', 'MEG1321'],
f2f_114: ['MEG1743',
'MEG0142', 'MEG0743', 'MEG1523', 'MEG2142',
'MEG1321', 'MEG2521'],
f2f_115: ['MEG0533','MEG1433', 'MEG1743',
'MEG0142', 'MEG0743', 'MEG0822', 'MEG2542', 'MEG1321'],
f2f_116: ['MEG1023', 'MEG1743',
'MEG0142', 'MEG1413', 'MEG1443', 'MEG2542',
'MEG1321', 'MEG1521'],
f2f_117: ['MEG0313', 'MEG1743', 'MEG2542',
'MEG0743', 'MEG1442', 'MEG1522', 'MEG1321',
'MEG1521', 'MEG2341'],
f2f_118: ['MEG1112', 'MEG1743',
'MEG2142', 'MEG2542', 'MEG2643', 'MEG1521', 'MEG1741'],
f2f_119: ['MEG0313', 'MEG1743',
'MEG2142', 'MEG2542', 'MEG2643', 'MEG1521', 'MEG1741',
'MEG2341'],
f2f_107sim2: ['MEG0332', 'MEG1743', 'MEG2542']
}
mf_autobad: True
mf_autobad_type: python
head_position_estimation:
coil_dist_limit: .005
coil_gof_limit: 0.98
coil_t_window: auto
coil_t_step_min: 0.1
movecomp: inter
annotations:
coil_bad_count_duration_limit: 0.5
rotation_limit: 10 # funloc uses 0.2
translation_limit: 0.1 # funloc uses .0001
sss:
sss_type: python
hp_type: python
filter_chpi: True
sss_regularize: in
int_order: 6
ext_order: 3
tsss_dur: 4.
st_correlation: 0.98
trans_to: twa
cont_hp: 25
cont_lp: 32
cont_hp_trans: 1.0
cont_lp_trans: 1.0
cont_as_esss: True
cont_reject: {'mag': 5.e-11, 'grad': 1.5e-9}
filtering:
lp_cut: 80.
lp_trans: 3.
filter_length: auto
fir_design: firwin
phase: zero
ssp:
proj_nums: {__default__: [[2, 2, 0], [0, 0, 0], [3, 3, 0]]}
proj_sfreq: 200
proj_meg: combined
eog_t_lims: [-0.25, 0.25]
ecg_t_lims: [-0.08, 0.08]
eog_f_lims: [1, 10]
ecg_f_lims: [5, 35]
proj_ave: True
get_projs_from: [0]
ssp_ecg_reject: null
ssp_eog_reject: null
ecg_channel: {
__default__: null, f2f_009: MEG0143,
f2f_010: MEG1713, f2f_024: MEG0113, f2f_030: MEG0143, f2f_036: MEG1711,
f2f_102: MEG1423, f2f_106: MEG1431, f2f_108: MEG1423
}
epoching:
tmin: 0.0
tmax: 1.0
bmin: 0.0
bmax: 1.0
t_adjust: -4.e-3
baseline: individual
decim: 10
analyses: ['All', 'Each']
in_names: &in_names
- talk
- ignore
in_numbers: &in_numbers
- 23
- 25
out_names: [['All'], *in_names]
out_numbers: [[1, 1], [1, 2]]
must_match: [[], [0, 1]]
autoreject_thresholds: True
autoreject_types: ['mag', 'grad']
reject_epochs_by_annot: True
reject_tmin: null
reject_tmax: null
epochs_proj: delayed
epochs_prefix: All_1sec
covariance:
cov_method: shrunk
compute_rank: True
cov_rank: null
force_erm_cov_rank_full: False
forward:
bem_type: 5120
src: oct6
src_pos: 5
forward_dir: forward_surf
trans_dir: raw_fif
inverse:
inv_names: ['%s']
inv_runs: [0]
inverse_dir: inverse_surf
report:
bem: False
covariance: False
drop_log: True
source: False
bem: False
source_alignment: True
good_hpi_count: True
whitening: [
{analysis: Each, name: talk, cov: '%s-80-sss-cov.fif'},
{analysis: Each, name: ignore, cov: '%s-80-sss-cov.fif'}
]
sensor: {analysis: All, name: All, times: [5, 10, 20, 40]}