script-files.md

 [[_TOC_]]
 
 # Introduction
-text here
+This plugin allows for users to combine scripts into pipelines, and run a series of process all at once on a set of data files. 
+```matlab
+%replace_string comments:
+%	in_fname_key = [in_fname_key] - key string for the input file..[batch_dfn,_,-1]_mrg.set
+%	in_path = [in_path] - Relative path to input data files assuming cd = work_path
+%	recur_sec = [init_recur_sec] - Recurrence (sec) for the original artifact detection epoching (e.g. .5)
+%	limit_sec = [init_limit_sec] - Limits (sec) for the original artifact detection epoching (e.g. [-.5 0])
+%	out_path = [out_path] - Relative path to output data files assuming cd = work_path
+%   ref_loc_file = [ref_loc_file] - name of the file containing the reference channel locations (including the relative path)
+%	low_bound_hz = [low_bound_hz] - Low bound of the filter bass-band
+%	high_bound_hz = [high_bound_hz] - Upper bound of the filter bass-band
+%   recur_sec = [recur_sec] - Recurrence (sec) for the current artifact detection epoching (e.g. .5)
+%   limit_sec = [limit_sec] - Limits (sec) for the current artifact detection epoching (e.g. [-.5 .5])
+%	epoch_z = [epoch_z] - z threshold for flagging channel during icsd criteria (e.g. 3)
+%	epoch_p = [epoch_p] - Percentage of flagged components required to flag an epoch during icsd criteria (e.g. .1)
+%	epoch_trim = [epoch_trim] - Percentage trim for confidence intervals during channel neighbour r criteria (10 = 5% top and bottom)
+%	min_gap_ms = [min_gap_ms] - Minimum time (ms) to allow between periods marked for rejection 
+```
+
+```matlab
+%%LOAD DATASET... 
+disp('Loading set file: [batch_dfn]...');
+tic;
+EEG = pop_loadset('filename','[batch_dfn]','filepath','[in_path]');
+EEG = eeg_checkset( EEG );
+disp('TIME TO: LOAD DATASET...');
+toc
+```
+
+
+```matlab
+%%SAVE IC DATA SET...
+tic;
+EEG = pop_saveset( EEG, 'filename','[batch_dfn,_,-1]_comp2.set','filepath','[out_path]');
+disp('TIME TO: SAVE IC DATA SET...');
+toc
+```
+
+
+```matlab
+%%FILTER HIGH PASS...
+disp('High pass filtering the data...');
+tic;
+EEG=pop_eegfiltnew(EEG,[],[low_bound_hz],[],true,[],0);
+EEG.setname='filtHP';
+EEG = eeg_checkset( EEG );
+disp('TIME TO: FILTER HIGH PASS...');
+toc
+```
+
+```matlab
+% remove comps manually
+disp('REMOVE MARKS AND COMPS');
+% remove marks
+
+%WAIT FOR SCROLL PLOT TO CLOSE...
+uiwait;
+```
+
 ![PIPLELINE_CHART](/uploads/462408d7a3e809082e2bb8f8d2ee4504/PIPLELINE_CHART.png)
 text here
 # Saving scripts (*.htb files)