| ... | ... | @@ -22,22 +22,22 @@ This section is designed to outline the key procedures of each of the pipeline s |
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| [in_path] | [] | Relative path to input data files assuming cd = work_path |
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| [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). |
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| [staging script] | derivatives/lossless/code/scripts/staging_script.m | Script file path/name that creates marks based on events in the raw data file. |
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| [staging_script] | derivatives/lossless/code/scripts/staging_script.m | Script file path/name that creates marks based on events in the raw data file. |
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| [recur_sec] | 1 | Recurrence (sec) for artifact detection epoching |
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| [limit_sec] | [0 1] | Limits (sec) for artifact detection epoching |
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| [sd_t_meth] | q | Method used for flagging epochs (e.g. 'q' (quantiles), or 'na') |
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| [sd_t_vals] | [.3 .7] | Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7]) |
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| [sd_t_o] | 6 | z threshold for flagging epochs during standard deviation criteria |
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| [sd_t_f_meth] | fixed | Fixed method used for flagging epochs (should be 'fixed') |
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| [sd_t_f_vals] | | Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed') |
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| [sd_t_f_o] | 0.2 | z threshold for flagging epochs during fixed standard deviation criteria |
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| [sd_t_meth] | q | Method used for **identifying** outlying epochs (e.g. 'q' (quantiles), 'z' (z-score), or 'na') |
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| [sd_t_vals] | [.3 .7] | Percentage trim for confidence intervals during epoch std/quantile criteria for **identifying** outlying epochs (e.g. [.3 .7]) |
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| [sd_t_o] | 6 | threshold for number of standard deviations or quantiles from the mean for **identifying** outlying epochs |
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| [sd_t_f_meth] | fixed | Method used for **flagging** epochs. Can be 'fixed', or a distribution of values ('z-score' or 'q') |
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| [sd_t_f_vals] | | Percentage trim for confidence intervals during std/quantile criteria for **flagging** outlying epochs (e.g. [.3 .7], leave empty for 'fixed') |
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| [sd_t_f_o] | 0.2 | Threshold for **flagging** epochs (percentage for how many flagged channels are required for rejection of an epoch) |
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| [sd_t_pad] | 1 | Number of windows to pad onto each side of the ch_sd time flag |
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| [sd_ch_meth] | q | Method used for flagging channels (e.g. 'q' (quantiles), or 'na') |
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| [sd_ch_vals] | [.3 .7] | Percentage trim for confidence intervals during channel standard deviation criteria (e.g. [.3 .7]) |
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| [sd_ch_o] | 6 | z threshold for flagging channels during standard deviation criteria |
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| [sd_ch_f_meth] | fixed | Fixed method used for flagging channels (should be 'fixed') |
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| [sd_ch_f_vals] | | Percentage trim for confidence intervals during channel standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed') |
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| [sd_ch_f_o] | 0.2 | z threshold for flagging channel during fixed standard deviation criteria
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| [sd_ch_meth] | q | Method used for **identifying** outlying channels (e.g. 'q' (quantiles), 'z' (z-score), or 'na') |
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| [sd_ch_vals] | [.3 .7] | Percentage trim for confidence intervals during channel std/quantile criteria for **identifying** outlying epochs (e.g. [.3 .7]) |
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| [sd_ch_o] | 6 | threshold for number of standard deviations or quantiles from the mean for **identifying** outlying channels |
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| [sd_ch_f_meth] | fixed | Method used for **flagging** channels. Can be 'fixed', or a distribution of values ('z-score' or 'q') |
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| [sd_ch_f_vals] | | Percentage trim for confidence intervals during std/quantile criteria for **flagging** outlying channels (e.g. [.3 .7], leave empty for 'fixed') |
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| [sd_ch_f_o] | 0.2 | Threshold for **flagging** channels (percentage for how many flagged epochs are required for rejection of a channel) |
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| [ref_loc_file] | derivatives/lossless/code/misc/standard_1020_bucanl19.elc | Name of file containing the reference locations (including the relative path) |
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| [low_bound_hz] | 1 | Lower bound of the filter bass-band |
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| [high_bound_hz] | | Upper bound of the filter bass-band |
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| ... | ... | @@ -140,7 +140,7 @@ Versions |
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***
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*Updated/Verified by Mike Cichonski on 2019-03-14*
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*Updated/Verified by Mike Cichonski on 2019-04-04*
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[ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg/wikis/home) |
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