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 ## Parameters ##
 When performing a fNIRS analysis, these parameters are some of the most important settings and it is crucial that they are correct for the study that is being performed. FLARES exposes most of the parameters needed for an analysis allowing for immense customizability. These parameters have been broken down into subcategories in an attempt to keep them simple. These parameters are also shown in the order that they will be applied, and logical values have been applied by default. Below is a list of the submenus:
 - [Preprocessing](#preprocessing)
-- [Trimming](https://git.research.dezeeuw.ca/tyler/flares/wiki#trimming)
-- [Verify Optode Placement](https://git.research.dezeeuw.ca/tyler/flares/wiki#verify-optode-placement)
-- [Short/Long Channels](https://git.research.dezeeuw.ca/tyler/flares/wiki#shortlong-channels)
-- [Heart Rate](https://git.research.dezeeuw.ca/tyler/flares/wiki#heart-rate)
-- [Scalp Coupling Index](https://git.research.dezeeuw.ca/tyler/flares/wiki#scalp-coupling-index)
-- [Signal to Noise Ratio](https://git.research.dezeeuw.ca/tyler/flares/wiki#signal-to-noise-ratio)
-- [Peak Spectral Power](https://git.research.dezeeuw.ca/tyler/flares/wiki#peak-spectral-power)
-- [Coefficient of Variation](https://git.research.dezeeuw.ca/tyler/flares/wiki#coefficient-of-variation)
-- [Median Absolute Deviation](https://git.research.dezeeuw.ca/tyler/flares/wiki#median-absolute-deviation)
-- [Power Spectral Density Noise](https://git.research.dezeeuw.ca/tyler/flares/wiki#power-spectral-density)
-- [Channel Variance](https://git.research.dezeeuw.ca/tyler/flares/wiki#channel-variance)
-- [Bad Channels Handling](https://git.research.dezeeuw.ca/tyler/flares/wiki#bad-channels-handling)
-- [Optical Density](https://git.research.dezeeuw.ca/tyler/flares/wiki#optical-density)
-- [Temporal Derivative Distribution Repair filtering](https://git.research.dezeeuw.ca/tyler/flares/wiki#temporal-derivative-distribution-repair-filtering)
-- [Wavelet filtering](https://git.research.dezeeuw.ca/tyler/flares/wiki#wavelet-filtering)
-- [Haemoglobin Concentration](https://git.research.dezeeuw.ca/tyler/flares/wiki#haemoglobin-concentration)
-- [Enhance Negative Correlation](https://git.research.dezeeuw.ca/tyler/flares/wiki#enhance-negative-correlation)
-- [Filtering](https://git.research.dezeeuw.ca/tyler/flares/wiki#filtering)
-- [Extracting Events](https://git.research.dezeeuw.ca/tyler/flares/wiki#extracting-events)
-- [Epoch Calculations](https://git.research.dezeeuw.ca/tyler/flares/wiki#epoch-calculations)
-- [Design Matrix](https://git.research.dezeeuw.ca/tyler/flares/wiki#design-matrix)
-- [General Linear Model](https://git.research.dezeeuw.ca/tyler/flares/wiki#general-linear-model)
-- [Finishing Touches](https://git.research.dezeeuw.ca/tyler/flares/wiki#finishing-touches)
-- [Other](https://git.research.dezeeuw.ca/tyler/flares/wiki#other)
+- [Trimming](#trimming)
+- [Verify Optode Placement](#verify-optode-placement)
+- [Short/Long Channels](#shortlong-channels)
+- [Heart Rate](#heart-rate)
+- [Scalp Coupling Index](#scalp-coupling-index)
+- [Signal to Noise Ratio](#signal-to-noise-ratio)
+- [Peak Spectral Power](#peak-spectral-power)
+- [Coefficient of Variation](#coefficient-of-variation)
+- [Median Absolute Deviation](#median-absolute-deviation)
+- [Power Spectral Density Noise](#power-spectral-density)
+- [Channel Variance](#channel-variance)
+- [Bad Channels Handling](#bad-channels-handling)
+- [Optical Density](#optical-density)
+- [Temporal Derivative Distribution Repair filtering](#temporal-derivative-distribution-repair-filtering)
+- [Wavelet filtering](#wavelet-filtering)
+- [Haemoglobin Concentration](#haemoglobin-concentration)
+- [Enhance Negative Correlation](#enhance-negative-correlation)
+- [Filtering](#filtering)
+- [Extracting Events](#extracting-events)
+- [Epoch Calculations](#epoch-calculations)
+- [Design Matrix](#design-matrix)
+- [General Linear Model](#general-linear-model)
+- [Finishing Touches](#finishing-touches)
+- [Other](#other)
 
 Information about the individual parameters can be found by chicking the "?" icon next to the respective parameter, or below in the Performing an Analysis section. There are more popups and menus that will appear after the analysis has completed. They will be discussed further down.