ICA.md

@@ -7,55 +7,30 @@ The default and most used algorithm in EEG/MEG is infomax.
 * This plugin can be run using the command line
 * Can use the current montage instead of raw channels.
 * Can filter signals before computing.
+* Can decimate the number of samples to speed up computation (not recommended)
+* The user can specify artifacted sections to reject.
+* The user can specify data chunks to use (and not the entire data file).
 
+# Parameters
+![image](uploads/cda917c7d52d42b24d5d0745f9c04498/image.png)
+**Data Input section:**
+The default is to compute on raw channels (channels present in file avoiding any montage).  
+Use current Montage option allows computing on current montage.
 
+Modality option is usefull only for simulateneous recordings (EEG and MEG for example)
 
-# Running the process
+Bad channels are ignored by default.
 
-![image](/anywave/documentation/-/wikis/uploads/9ad546ff593f3974b9208450b546d4b6/image.png)
-
-## Select algorithm
-
-![image](/anywave/documentation/-/wikis/uploads/e5c0821ef27065f2789a9f95b74b6e43/image.png)
-
-Currently only two algorithms are available: infomax and sobi.\
-Note that depending on the selected algorithm the Extra parameters section of the GUI may vary.
-
-## Filter the data (or not)
-
-You may apply high pass/low pass filters on data. If the values are set to zeros, a warning message will appear requesting a confirmation that you will process on raw data.\
-The Decimate Data is off by default. Check it on to speed up computation by removing some data points.
-
-## Select the channels
-
-![image](/anywave/documentation/-/wikis/uploads/af3b92d740c92c56bd5b7b4350a9a5e6/image.png)\
-You can process ICA on raw channels present on the current data file OR choose to compute only on channels present in the current Montage.
-
-If you process SEEG data you can also restrict the computation to a particular SEEG Electrode.
-
-## Avoid artefacts and/or compute only on some part of the data
-
-If the current file contains markers, you will see a Data Input Options appears in the GUI:\
-![image](/anywave/documentation/-/wikis/uploads/5f3f236d5493fb6ce5f55b59af24d1eb/image.png)
-
-You may use the options to avoid marked artefacted data and or restrict the computation on some marked parts of data.
-
-## Ignore bad channels
-
-That is the default behavior. If bad channels had been marked previously, they will be ignored during the computation.
-
-## Number of components
-
-By default the maximum of components will be extracted from the data.\
-You can however reduce the dimensions of the data (using a PCA) to get less components.
+## Data Input Section
+This is where you can select the data chunks to avoid and/or use.
 
 ## Output
-
+Select the number of independ components to extract.  
+Click the All Component to set if to the maximum possible value.
 If you are currently working on data stored in a BIDS the output MATLAB file will be stored in the derivatives folder of your BIDS.\
 If you are not working with BIDS the output MATLAB file will be generated in the current data file folder. The file name is BIDS alike providing useful information just by reading it.
 
 # MATLAB file description
-
 If you develop your own ICA algorithm in MATLAB, you can create a compatible file to load with AnyWave to see the components time series.\
 To do so you must create a file like the one AnyWave generates.