% sd_epoch_z = [sd_epoch_z] z threshold for flagging epochs during standard deviation criteria (e.g. 6)
% sd_t_meth = [sd_t_meth] Method used for flagging epochs (e.g. 'q' (quantiles), or 'na' (default))
% sd_epoch_p = [sd_epoch_p] Percentage of flagged channels required to flag an epoch during standard deviation criteria (e.g. .1)
% sd_t_vals = [sd_t_vals] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7])
% sd_epoch_trim = [sd_epoch_trim] Percentage trim for confidence intervals during epoch standard deviation criteria (10 = 5% top and bottom)
% sd_t_o = [sd_t_o] z threshold for flagging epochs during standard deviation criteria (e.g. 6)
% sd_epoch_pad = [sd_epoch_pad] Number of windows to pad onto each side of the ch_sd time flag
% sd_t_f_meth = [sd_t_f_meth] Fixed method used for flagging epochs (should be 'fixed')
% sd_chan_z = [sd_chan_z] z threshold for flagging channel during standard deviation criteria (e.g. 6)
% sd_t_f_vals = [sd_t_f_vals] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7], leave empty for 'fixed')
% sd_chan_p = [sd_chan_p] Percentage of flagged epochs required to flag a channel during standard deviation criteria (e.g. .1)
% sd_t_f_o = [sd_t_f_o] z threshold for flagging epochs during fixed standard deviation criteria (e.g. .2)
% sd_chan_trim = [sd_chan_trim] Percentage trim for confidence intervals during channel standard deviation criteria (10 = 5% top and bottom)
% sd_t_pad = [sd_t_pad] Number of windows to pad onto each side of the ch_sd time flag
% sd_ch_meth = [sd_ch_meth] Method used for flagging channels (e.g. 'q' (quantiles), or 'na' (default))
% sd_ch_vals = [sd_ch_vals] Percentage trim for confidence intervals during channel standard deviation criteria (e.g. [.3 .7])
% sd_ch_o = [sd_ch_o] z threshold for flagging channels during standard deviation criteria (e.g. 6)
% sd_ch_f_meth = [sd_ch_f_meth] Fixed method used for flagging channels (should be 'fixed')
% sd_ch_f_vals = [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 = [sd_ch_f_o] z threshold for flagging channel during fixed standard deviation criteria (e.g. 6)
% ref_loc_file = [ref_loc_file] Name of file containing the reference locations (including the relative path)
% ref_loc_file = [ref_loc_file] Name of file containing the reference locations (including the relative path)
% low_bound_hz = [low_bound_hz] Lower bound of the filter bass-band
% low_bound_hz = [low_bound_hz] Lower bound of the filter bass-band
% high_bound_hz = [high_bound_hz] Upper bound of the filter bass-band
% high_bound_hz = [high_bound_hz] Upper bound of the filter bass-band
% n_neighb_chan = [n_neighb_chan] Number of channels to use in nearest neighbour r calculation (for channel criteria)
% save_f_res = [save_f_res] 1 if you want to save the filter residuals (Default: 1)
% r_chan_z = [r_chan_z] z threshold for flagging channel during neighbour r criteria (e.g. 3)
% n_nbr_ch = [n_nbr_ch] Number of channels to use in nearest neighbour r calculation (for channel criteria)
% r_chan_p = [r_chan_p] Percentage of flagged epochs required to flag a channel during neighbour r criteria (e.g. .1)
% r_ch_meth = [sd_ch_meth] Method used for flagging low r channels (e.g. 'q' (quantiles), or 'na' (default))
% r_chan_trim = [r_chan_trim] Percentage trim for confidence intervals during channel neighbour r criteria (10 = 5% top and bottom)
% r_ch_vals = [sd_ch_vals] Percentage trim for confidence intervals during low r channel standard deviation criteria (e.g. [.3 .7])
% r_ch_o = [r_ch_o] z threshold for flagging channel during neighbour r criteria (e.g. 3)
% r_ch_f_meth = [r_ch_f_meth] Fixed method used for flagging low r channels (should be 'fixed')
% r_ch_f_vals = [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 = [r_ch_f_o] z threshold for flagging channel during fixed neighbour r criteria (e.g. 3)
% bridge_trim = [bridge_trim] Percentage trim for z calculation of bridged channels (e.g. 40 = 20% top and bottom)
% bridge_trim = [bridge_trim] Percentage trim for z calculation of bridged channels (e.g. 40 = 20% top and bottom)
% bridge_z = [bridge_z] z threshold for flagging channel during bridging criteria (e.g. 8)
% bridge_z = [bridge_z] z threshold for flagging channel during bridging criteria (e.g. 8)
% n_neighb_epoch = [n_neighb_epoch] Number of channels to use in nearest neighbour r calculation (for epoch criteria)
% n_nbr_t = [n_nbr_t] Number of channels to use in nearest neighbour r calculation (for epoch criteria)
% epoch_z = [epoch_z] z threshold for flagging epochs during neighbour r criteria (e.g. 3)
% r_t_meth = [r_t_meth] Method used for flagging low r epochs (e.g. 'q' (quantiles), or 'na' (default))
% epoch_p = [epoch_p] Percentage of flagged channels required to flag an epoch during neighbour r criteria (e.g. .1)
% r_t_vals = [r_t_vals] Percentage trim for confidence intervals during low r epoch standard deviation criteria (e.g. [.3 .7])
% epoch_trim = [epoch_trim] Percentage trim for confidence intervals during epoch neighbour r criteria (10 = 5% top and bottom)
% r_t_o = [r_t_o] z threshold for flagging epochs during neighbour r criteria (e.g. 3)
% r_t_f_meth = [r_t_f_meth] Fixed method used for flagging low r epochs (should be 'fixed')
% r_t_f_vals = [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 = [r_t_f_o] z threshold for flagging epochs during fixed neighbour r criteria (e.g. 3)
% min_gap_ms = [min_gap_ms] Minimum time (ms) to allow between periods marked for rejection
% min_gap_ms = [min_gap_ms] Minimum time (ms) to allow between periods marked for rejection
% out_path = [out_path] Relative path to output data files assuming cd = work_path
% out_path = [out_path] Relative path to output data files assuming cd = work_path
% amica_param_file = [amica_param_file] template amicadefs.param file to modify.
% amica_param_file = [amica_param_file] template amicadefs.param file to modify
% save_diff = [savediff] YES if you want to save the filter residuals (Default: NO)
% amica_threads_s02 = [amica_threads_s02] number of threads to use for running s02 amica script (Default: 8)
%% CHECK FOR OUTPUT PATH AND CRETAE IF NECESSARY
%% CHECK FOR OUTPUT PATH AND CRETAE IF NECESSARY
if ~exist('[out_path]/[batch_dfn,/,-1]','dir');
if ~exist('[out_path]/[batch_dfn,/,-1]','dir');
...
@@ -85,7 +97,7 @@ end
...
@@ -85,7 +97,7 @@ end
%warp locations to standard head surface:
%warp locations to standard head surface:
if ~isempty('[montage_info]');
if ~isempty('[montage_info]');
if isempty(str2num('[montage_info]'));
if isempty(str2num('[montage_info]'));
%if it is a BIDS channel tsv, load the tsv,
%if it is a BIDS channel tsv, load the tsv,sd_t_f_vals
%else read the file that is assumed to be a transformation matrix.
%else read the file that is assumed to be a transformation matrix.
% epoch_z = [epoch_z] z threshold for flagging channel during icsd criteria (e.g. 3)
% sd_t_meth = [sd_t_meth] Method used for flagging epochs (e.g. 'q' (quantiles), or 'na' (default))
% epoch_p = [epoch_p] Percentage of flagged components required to flag an epoch during icsd criteria (e.g. .1)
% sd_t_vals = [sd_t_vals] Percentage trim for confidence intervals during epoch standard deviation criteria (e.g. [.3 .7])
% epoch_trim = [epoch_trim] Percentage trim for confidence intervals during channel neighbour r criteria (10 = 5% top and bottom)
% sd_t_o = [sd_t_o] z threshold for flagging epochs during standard deviation criteria (e.g. 6)
% min_gap_ms = [min_gap_ms] Minimum time (ms) to allow between periods marked for rejection
% sd_t_f_meth = [sd_t_f_meth] Fixed method used for flagging epochs (should be 'fixed')
% amica_param_file = [amica_param_file] Template amicadefs.param file to modify.
% sd_t_f_vals = [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 = [sd_t_f_o] z threshold for flagging epochs during fixed standard deviation criteria (e.g. .2)
% out_path = [out_path] Relative path to output data files assuming cd = work_path
% out_path = [out_path] Relative path to output data files assuming cd = work_path
% min_gap_ms = [min_gap_ms] Minimum time (ms) to allow between periods marked for rejection
% amica_param_file = [amica_param_file] template amicadefs.param file to modify
% amica_threads_s04 = [amica_threads_s04] number of threads to use for running s04a, s04b, s04c amica scripts (Default: 8)
