Characteristics of respiratory measures in young adults scanned at rest, including systematic changes and "missed" deep breaths
Jonathan Power, Charles Lynch, Marc Dubin, Benjamin Silver, Alex Martin, Rebecca Jones
Neuroimage 2020 Jan 1; 204:116234
Below are movies and files associated with the article "Characteristics of respiratory measures in young adults scanned at rest, including systematic changes and "missed" deep breaths". All movies are 1080p and will look best at full-screen resolutions. The movies stream from YouTube. Click on links to download movies or files. Files to download are hosted on Dropbox Pro; if the links don't work our traffic has exceeded its 200GB/day limit and the links will be re-enabled the following day.
Data quality check:
A movie of the physiology traces of the 900-subject release Human Connectome Project (HCP) and decisions about whether data quality was sufficient for use was part of the supplemental material of another paper and can be found here. These traces and decisions are the basis of selecting 440 of the 900 subjects for analysis. The data analyzed are exactly the data examined in this paper.
Respiratory response functions (.zip)
In the link at the top of this section you can download text files of the Birn et al., 2008 RVT RRF, the Chang et al., 2009 RVT and RV RRFs, the RRF to spontaneous deep breath global signals measured from individual instances in Power et al., 2017 (NIH) and Power et al., 2018 (NA), and the deep breath global signals of instructed breaths in the present manuscript (CJL). Signals were calculated directly from published fits for the Birn et al., 2008 RRF, and measured empirically from the published plots of Chang et al., 2009, with subsequent checking by Catie Chang.
Matlab wrapper for RVT calculations (.zip)
RVT can be complicated to calculate due to peakfinding settings and sampling procedures. Implementations of RVT exist in FSL and AFNI, and we coded a "core" implementation in Matlab as well as the full algorithm proposed by Rasmus Birn. A small demo package that calculates all four versions is provided with a substrate physiology file. Users may need to alter the FSL directory settings at the top of the script for the demo to work. Sampling rates are hard coded at 400 HZ and 720 ms TRs in variables at the top of the script, which would need modification to work with data with different sampling rates. Code was written by Charles Lynch, direct questions to him at: firstname.lastname@example.org.
Movie 1: (.mov - 1.4 GB)
This movie illustrates each run of the 440 analyzed subjects. At top the first panel shows head position traces (gray) and motion traces (red= FDfiltered,4-TR, light red = FDfiltered), the second panel shows DVARS traces before (light green) and after (dark green) FIX-ICA, the third panel shows in blue the respiratory belt trace and the derived ENV (red), RV (blue) and RVT (black) traces. The fourth panel shows as a grayscale heat map all in-brain time series of the image before and after FIX-ICA (as successive frames of the movie).
Movie 2 (.mov - 8 MB)
These movies show the 15 deep breaths of Figure 5. 15 gray plots for each pattern are shown, from different subjects, with vertical red lines denoting the 90 seconds of data examined and t = 0.