# Automated Processing of fNIRS Data--A Visual Guide to the Pitfalls and Consequences
## Results
### GLM Analysis  
We divided our results into three different ways of evaluating significant channels. Specifically, we concentrated on only oxy- or only deoxyhemoglobin (Figure 11a) as well as on regarding a channel only as significant if there is a significant increase in oxy- accompanied by a decrease in deoxyhemoglobin in the same channel (Figure 11b). Figure 11 shows how many times a channel was regarded as significant over all participants in percentage (Figure 11, boxplots). Outliers are shown as red \"+\" outside the boxplots 95 th percentile and the ROI channels 4, 5, 10, and 12 are shown as colored circles  
Figure 10: Evaluation of LF methods in regard to Cohen’s d and contrast to noise ratio. (**A**) Mean and standard deviation for maximum Cohen’s d value in the ROI (channels 4, 5, 10 and 12) is presented for no de-noising as well as all three LF de-noising methods. No significant difference was found. (**B**) Mean and standard deviation for maximum contrast to noise ratio (CNR) in the ROI. Red represents oxy- and blue deoxyhemoglobin measures. Each circle represents the maximum value for one subject. (yellow, purple, orange, and blue, respectively); the black larger circle represents the percentage of times the ROI was activated over all participants (regardless of which or how many channels within the ROI were significantly activated). For oxyhemoglobin alone, 88% of participants had significant activation in the ROI without de-noising, with SSD* and PCA and 100% with GloAvg. For deoxyhemoglobin, 88% of participants had significant activation in the ROI without any LF de-noising and PCA, 81% with SSD* de-noising and 94% with GloAvg. For the combination of significant oxy- and deoxyhemoglobin activation (Figure 11b), 75% of participants had significant activation in the ROI without any LF de-noising and with SSD*, 81% with PCA and 94% of participants had significant activation when using GloAvg. The 4 ROI channels and their highest number of activation can be found in Table 1 and Figure 12). Mean percentage \(\pm\) standard deviation of significant channels outside of the ROI for oxy-, deoxyhemoglobin and combined were 33 \(\pm\) 9, 26 \(\pm\) 13 and 11 \(\pm\) 10 for None (no LF de-noising); 30 \(\pm\) 12, 23 \(\pm\) 13 and 9 \(\pm\) 8 for SSD*; 30 \(\pm\) 10; 28 \(\pm\) 12 10 \(\pm\) 10 for PCA; and for GloAvg de-noising 22 \(\pm\) 10, 30 \(\pm\) 12 and 12 \(\pm\) 10%, respectively. Significant lower results were found with channels outside the ROI when combining oxy- and deoxyhemoglobin instead of oxy- or deoxyhemoglobin alone for all methods (\(p_{\mathrm{c}}\) < 0.000). Differences were also found between oxy- and deoxyhemoglobin alone for all de-noising methods except PCA: None (\(p_{\mathrm{c}}\) = 0.0007), SSD (\(p_{\mathrm{c}}\) = 0.019), PCA (\(p_{\mathrm{c}}\) = 0.38) and GloAvg (\(p_{\mathrm{c}}\) = 0.001). For the combined hemoglobin condition, the different de-noising methods were significantly higher within the ROI for PCA (\(p_{\mathrm{c}}\) = 0.0005) and GloAvg (\(p_{\mathrm{c}}\) = 0.032) in comparison to no de-noising. No difference was found between: no de-noising vs. SSD* (\(p_{\mathrm{c}}\) = 0.38); SSD* vs. PCA (\(p_{\mathrm{c}}\) = 0.75); SSD* vs. GloAvg (\(p_{\mathrm{c}}\) = 0.93); PCA vs. GloAvg (\(p_{\mathrm{c}}\) = 0.36) (Figure 11, not marked). In addition, the highest \(t\)-stats did not differ significantly between methods (Figure 11b). We also ran the same GLM analysis without including derivatives (Figure 13). In the oxy- and deoxyhemoglobin combined condition significant lower activity in the ROI over all participants was  
Figure 11: GLM analysis results. **(A)** Results were evaluated with oxy- or deoxyhemoglobin only, (B) as well as combined, i.e., when a channel showed a significant increase in oxy- accompanied by a significant decrease in deoxyhemoglobin. The figure shows how many times (in percentage) a channel was regarded as significant over all participants.