essinit.md

@@ -64,8 +64,8 @@ The table below indicates with an **x** the methods in which you can describe ea
 | modality       |     x  |       |        |    x   |    x   | System used for recording                                                       |
 | oneloc         |  x     |       |      |    x   |    x   | 1 if you are using a single montage location file, 0 for subject specific files |
 | locs_file_name |      x  |       |        |    x   |    x   | Path to montage or naming convention for subject specific files                 |
-| NotEEG_chans   |   x  |       |        |    x   |        | Channel numbers that do not contain EEG data                                    |
-| Fid_chans      |     x  |      |        |    x   |    x   | Channel numbers of the Fiducials for warping reference                          |
+| remData   |   x  |       |        |    x   |        | Channel numbers that do not contain EEG data and need to be removed before location file is loaded                                   |
+| remChans      |     x  |      |        |    x   |      | Channel numbers of the Fiducials or other channels that are not in the data                       |
 | ref_loc_file   |       |    x   |        |    x   |        | Warp  reference surface, default is the MNI head if no config is given                               |
 | tMatrix        |      |    x   |    x   |    x   |    x   | Matrix used to warp your location files to MNI head                             |
 | mergefiles       |       |    x   |    x   |    x   |    x   | A list of the names of the files you wish to merge using swap strings. Leave blank for browsing                          |
@@ -122,12 +122,10 @@ If you leave the config empty ```''``` the following GUI will be displayed. Simp
 
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-**NotEEG_chans**  
-These are the channel indices that do not contain EEG information this includes unplugged channels but will **not include fiducials**. ESS will by default not load any channels that do not contain EEG. For example our lab never uses the EXG8 channel of our BioSemi, this corresponds to using ```[NotEEG_chans],[140]``` to remove the very last channel. This item is one of the few that does not contain a backup GUI as an empty config is a acceptable answer and this default will remove no channels. 
+**remData**  
+These are the channel indices that do not contain EEG information this includes unplugged channels but will **not include fiducials**. ESS will by default not load any channels that do not contain EEG. For example our lab never uses the EXG8 channel of our BioSemi so there is meaningless data in its EEG.data row, this corresponds to using ```[remData],[136]``` (128 electrodes + 7 eyes + 1 junk) to remove the very last channel. This item is one of the few that does not contain a backup GUI as an empty config is a acceptable answer and this default will remove no channels. 
 
-Note that the channels that are purged/removed are: **NotEEG_chans + Fid_chans(see below)**, so channels should only be included in one or the other.
-
-:so: This feature will depend on your labs modality. It is good practice to load a raw file and investigate the EEG.chan_locs structure.  
+:so: This feature will depend on your labs modality. It is good practice to load a raw file and investigate the EEG.data structure.  
 
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@@ -153,7 +151,7 @@ This item allows you to down sample your data's sampling rate. Use ```[change_sr
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 **erename**    
-This variable stands for *Event-Rename* and can be used several different ways.
+This variable stands for *Event-Rename* and can be used several different ways:
 
 **1. ESS**   
 This config field can be left blank, all you event codes will be renamed to their designated labels found in the study description.
@@ -186,9 +184,8 @@ The next example has a range of codes for each image for example *house_up* is c
 
 # Warping Variables
 
-**Fid_chans**  
-This item is very similar to **NotEEG_chans** but is a list  of the indices of the fiducials. ESS capsules denote this information by specifying the channel *Type* as *FID* and will automatically use these when warping , but if you are using config you will have to specify these. For example our lab uses the first three channel locations as the LPA, NZ and RPA fiducials, using```[Fid_chans],[1 2 3]``` will set these as the landmarks for warping and then remove them from EEG.data afterwards. If you the leave config empty the following GUI will be displayed. Simply type in a indices of the channels, you do not have to do [  ] brackets in the GUI as it is already expecting a matrix. For example type```1 2 3```.
-![fids](/uploads/bc2b77cfce9682a2f667151421c71670/fids.png)
+**remChans**  
+The indecies listed will be set as *not EEG data* and placed in the *EEG.chaninfo.nodatchans* rather than *EEG.chanlocs* when the location file is loaded. ESS capsules denote this information by specifying the channel *Type* as *FID* and will automatically use these when warping , but if you are using config you will have to specify these. For example our lab uses the first three channel locations as the LPA, NZ and RPA fiducials, and the CMS and DRL are near the end. Using```[remChans],[1 2 3 132 133]```will properly load these.
 
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