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Welcome to processFNIRS v0.4

This tool is designed to allow modular processing of fNIRS data. If this is your first time using this software, try running processFNIRS2() and click configure methods to build your first methods file. You will need to load the default functions first, but then you may add functions to your library and build your first processing methods. Test out a few methods using the visualization tool to see how they work!

Note: settings changed in the GUI do not affect your data and are for visualization only.

Once you have defined a few functions you can use the normal processFNIRS2 pipeline.

This is generally done in three stages:

1) Import Data
	Import your data using processFNIRS.Import.ImportNIR (or other function)
	Load your data using the function as a string or select the file yourself
	ex: mydata = processFNIRS.Import.ImportNIR('myNIRSfile.nir')

2) Set Methods
	Select a method for both Raw and Oxy domain processing
	You can visualize the effects of your methods by using processFNIRS(mydata)
	and configure your methods by using processFNIRS.Methods.Oxy/Raw.ConfigureMethods
	Selecting methods is easy, you can select a method using either the method name,
	Or selecting the method interactively
	Please note that both the Raw method is applied first and then the Oxy method
	ex: processFNIRS2.Methods.Raw.SetMethod('MyMethodName')
	ex: processFNIRS2.Methods.Oxy.SetMethod('MyMethodName')

3) Process Data
	Run your processing method on your data using processFNIRS2(mydata)
	You can optionally process only the oxy or raw domain signals using processFNIRS2.Process.ProcessRaw/ProcessOxy
	However the default function will run both Raw and Oxy pipelines
	exL myprocesseddata=processFNIRS2(mydata))

processfNIRS2 is laid out in the following manner    

Function	Description
processFNIRS2	Main function (runs GUI if no assignment)
*Data	functions to manipulate individual fNIRS segments
-ApplyChannelMask	Sets data in rejected channels to NaN
-GetMarkers	Function to find the timepoints of markers in a regex style
-Resample	Function to resample or average fNIRS data (ex     30s block average or convert to 1hz)
-SetT0	Function to shift the fNIRS time to match start of experiment t=0
-Split	Function to split fNIRS segment based on different input times
*GUI	Shortcut for accessing the GUI
*Help	Access in-program help information
*Import	Functions to import fNIRS files
-ImportHitachiMES	Import Hitachi Probes
-ImportNIRx	Import NIRx files
-ImportNIR	Import fNIR Devices/Biopac files
-ImportSampleData	Import some sample data included here
*Methods	Functions to change and modify processing methods
-Oxy	Oxy conversion pipeline methods
-ConfigureMethods	GUI to edit functions in Oxy pipeline
-ImportMethods	Import pre-existing methods from a file
-List	List currently loaded methods
-SetMethod	Select a method based on name or method number
-Raw	Raw conversion pipeline methods
ConfigureMethods	GUI to edit functions in Oxy pipeline
ImportMethods	Import pre-existing methods from a file
List	List currently loaded methods
SetMethod	Select a method based on name or method number
-Process	Process fNIR segment data
-ProcessOxy	Run the Oxy Pipeline only (raw must be run first)
-ProcessRaw	Run the Raw Pipeline only
-Settings	Change settings related to processing
Baseline	Change baseline time settings
DPF	Change mode of Differential Path Length (DPF)
SetFixedDFP	Change to fixed distance factor
SetDPFmode	Set to 'none','fixed', or 'calc'
SelectDevice	Forcibly reload device settings for FNIRS probe

Please be sure to add the matlab path the main folder (processFNIRS2) and the folders named    

  base_functions, GUI, and functions

Folders with + signs in front of the name do not need to be included

base_functions and GUI contain functions related to the operation of processFNIRS2

functions contains the functions used in the processFNIRS2 method pipelines, but you may use any matlab functions in a pipeline if you add the function to your method

Loaded functions and methods are stored in the matlab preference directory

You may find these settings using the matlab command     prefdir

If you are having trouble loading processFNIRS2, delete these files and try again

processFNIRS2 is free for academic and non-commercial use, but some included code may have other licenses

(c)2019

Contact Adrian Curtin for more information at abc48@drexel.edu