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  • bucanl_pipelines
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  • pipeline scripts

Last edited by Mike Cichonski Apr 04, 2019
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pipeline scripts

  • Pipeline Scripts
  • Scalpart (s01)
  • Amica (s02, s04a, s04b, s04c)
  • Compart (s03)
  • Concat and Dipfit (s05)

Pipeline Scripts

This section is designed to outline the key procedures of each of the pipeline scripts.

Scalpart (s01)

  1. Load an initialized *_eeg.set file
  2. Standard Deviation or quantiles used to reject comically bad epochs (% goes to bad channel)
  3. Re-reference to interpolated average site of MNI surface: without flagged channels
  4. High pass filter
  5. Low pass filter
  6. Nearest Neighbour R on epochs, % goes to bad channel
    • low correlation
    • too high
  7. Rank channel - highest correlation removed
  8. ALL BAD CHANNELS FLAGGED
  9. Re-reference to interpolated average site of MNI surface: without all flagged channels
  10. Nearest Neighbour R on epochs for time removal
    • low correlation only by time segment
  11. Save an *_sa.set file
Variable Default in Config File Description
[in_path] [] Relative path to input data files assuming cd = work_path
[montage_info] Montage information to fit channel locations on a standard surface. This can be a transformations matrix (e.g. [-.14,-22,-48,-.07,0,-1.57,1080,1260,1240]), or a a file containing a transformation matrix (e.g. [batch_dfn]_transmat.mat), or a BIDS channel location tsv file (assuming that during BIDS init the channels were coregistered to the standard surface).
[staging script] derivatives/lossless/code/scripts/staging_script.m Script file path/name that creates marks based on events in the raw data file.
[recur_sec] 1 Recurrence (sec) for artifact detection epoching
[limit_sec] [0 1] Limits (sec) for artifact detection epoching
[sd_t_meth] q Method used for flagging epochs (e.g. 'q' (quantiles), or 'na')
[sd_t_vals] [.3 .7] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7])
[sd_t_o] 6 z threshold for flagging epochs during standard deviation criteria
[sd_t_f_meth] fixed Fixed method used for flagging epochs (should be 'fixed')
[sd_t_f_vals] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
[sd_t_f_o] 0.2 z threshold for flagging epochs during fixed standard deviation criteria
[sd_t_pad] 1 Number of windows to pad onto each side of the ch_sd time flag
[sd_ch_meth] q Method used for flagging channels (e.g. 'q' (quantiles), or 'na')
[sd_ch_vals] [.3 .7] Percentage trim for confidence intervals during channel standard deviation criteria (e.g. [.3 .7])
[sd_ch_o] 6 z threshold for flagging channels during standard deviation criteria
[sd_ch_f_meth] fixed Fixed method used for flagging channels (should be 'fixed')
[sd_ch_f_vals] Percentage trim for confidence intervals during channel standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
[sd_ch_f_o] 0.2 z threshold for flagging channel during fixed standard deviation criteria
[ref_loc_file] derivatives/lossless/code/misc/standard_1020_bucanl19.elc Name of file containing the reference locations (including the relative path)
[low_bound_hz] 1 Lower bound of the filter bass-band
[high_bound_hz] Upper bound of the filter bass-band
[save_f_res] 1 1 if you want to save the filter residuals
[n_nbr_ch] 3 Number of channels to use in nearest neighbour r calculation (for channel criteria)
[r_ch_meth] q Method used for flagging low r channels (e.g. 'q' (quantiles), or 'na')
[r_ch_vals] [.3 .7] Percentage trim for confidence intervals during low r channel standard deviation criteria (e.g. [.3 .7])
[r_ch_o] 6 z threshold for flagging channel during neighbour r criteria (e.g. 3)
[r_ch_f_meth] fixed Fixed method used for flagging low r channels (should be 'fixed')
[r_ch_f_vals] Percentage trim for confidence intervals during low r channel standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
[r_ch_f_o] 0.2 z threshold for flagging channel during fixed neighbour r criteria (e.g. 3)
[bridge_trim] 40 Percentage trim for z calculation of bridged channels (e.g. 40 = 20% top and bottom)
[bridge_z] 6 z threshold for flagging channel during bridging criteria
[n_nbr_t] 3 Number of channels to use in nearest neighbour r calculation (for epoch criteria)
[r_t_meth] q Method used for flagging low r epochs (e.g. 'q' (quantiles), or 'na')
[r_t_vals] [.3 .7] Percentage trim for confidence intervals during low r epoch standard deviation criteria (e.g. [.3 .7])
[r_t_o] 6 z threshold for flagging epochs during neighbour r criteria (e.g. 3)
[r_t_f_meth] fixed Fixed method used for flagging low r epochs (should be 'fixed')
[r_t_f_vals] Percentage trim for confidence intervals during low r epoch standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
[r_t_f_o] 0.2 z threshold for flagging epochs during fixed neighbour r criteria
[min_gap_ms] 2000 Minimum time (ms) to allow between periods marked for rejection
[out_path] [] Relative path to output data files assuming cd = work_path
[amica_param_file] derivatives/lossless/code/misc/amica15_default.param template amicadefs.param file to modify
[amica_threads_s02] 8 number of threads to use for running s02 amica script

diag111

diag222

diag333

Amica (s02, s04a, s04b, s04c)

The Amica script is run once initially, and then three more times in parallel after the component artefact rejection to ensure that the Amica procedure is replicable if run multiple times on the same dataset.

Versions

  • amica_init (s02)
  • amica_A,B,C (s04a, s04b, s04c)
Variable Default in Config File Description
[dep_path] derivatives/lossless/code/dependencies/eeglab_asr_amica/plugins/amica Relative path to amica executable program assuming cd = work_path
[in_path] [] Relative path to input data files assuming cd = work_path
[amica_ver] amica15 Name of the amica executable program version

Compart (s03)

Versions

  • compart_data (s03)
Variable Default in Config Description
[in_path] derivatives/lossless Path to input and output data files assuming cd = work_path
[recur_sec] 1 Recurrence (sec) for artifact detection epoching
[limit_sec] [0 1] Limits (sec) for artifact detection epoching
[sd_t_meth] q Method used for flagging epochs (e.g. 'q' (quantiles), or 'na')
[sd_t_vals] [.3 .7] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7])
[sd_t_o] 6 z threshold for flagging epochs during standard deviation criteria (e.g. 6)
[sd_t_f_meth] fixed Fixed method used for flagging epochs (should be 'fixed')
[sd_t_f_vals] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
[sd_t_f_o] 0.2 z threshold for flagging epochs during fixed standard deviation criteria (e.g. .2)
[out_path] derivatives/lossless Relative path to output data files assuming cd = work_path
[min_gap_ms] 2000 Minimum time (ms) to allow between periods marked for rejection
[amica_param_file] derivatives/lossless/code/misc/amica_default.param Template amicadefs.param file to modify
[amica_threads_s04] 8 number of threads to use for running s04a, s04b, s04c amica scripts

diag444

Concat and Dipfit (s05)

Versions

  • concat_data (s05)
Variables Default in Config Description
[in_path] derivatives/lossless Relative path to input data files assuming cd = work_path
[recur_sec] 1 Recurrence (sec) for the current artifact detection epoching
[limit_sec] [0 1] Limits (sec) for the current artifact detection epoching
[sd_t_meth] q Method used for flagging epochs (e.g. 'q' (quantiles), or 'na')
[sd_t_vals] [.3 .7] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7])
[sd_t_o] 6 z threshold for flagging epochs during standard deviation criteria (e.g. 6)
[sd_t_f_meth] fixed Fixed method used for flagging epochs (should be 'fixed')
[sd_t_f_vals] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
[sd_t_f_o] 0.2 z threshold for flagging epochs during fixed standard deviation criteria (e.g. .2)
[min_gap_ms] 2000 Minimum time (ms) to allow between periods marked for rejection
[icr_crit] 0.05 False discovery rate of component replicatablilty, measure of sensitivity %
[dip_vol] derivatives/lossless/code/misc/standard_vol.mat file path/name of the standard volume file used in dipole fitting
[dip_mri] derivatives/lossless/code/misc/standard_mri.mat file path/name of the standard mri file used in dipole fitting
[dip_elc] derivatives/lossless/code/misc/standard_1020.elc file path/name of the standard electrode file used in dipole fitting
[dip_transmat] [0 0 0 0 0 0 1 1 1] Transformation matrix to apply during dipole fit
[cor_transmat] [0,0,0,0,0,1.57,1,1,1] The transformation matrix to apply between dipole fitting to the standard head and performing ICLabel to the EEGLAB default orientation
[cor_nosedir] +X Nose direction of montage to apply between dipole fitting to the standard head and performing ICLabel to the EEGLAB default orientation (e.g. +Y)
[out_path] derivatives/lossless Relative path to output data files assuming cd = work_path

Updated/Verified by Mike Cichonski on 2019-03-13

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