fNIRS Course – DAY 4 – October 22, 2020

DAY 4 – October 22
10:00 am – 12:00 pm ET

– Motion Artifacts
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LECTURE AND EXERCISE

DAY 4 Videos and Zoom Chat:

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David Boas
David Boas (@dboas)
14 hours ago

It was suggested that we consider implementing this motion correction method in Homer. They apparently have matlab code available for it.
Does anyone have experience using this method? Their result that CBSI is better than spline-SG is not consistent with our experience.

Fishburn, F., Ludlum, R., Vaidya, C., Medvedev, A. (2019). Temporal Derivative Distribution Repair (TDDR): A motion correction method for fNIRS NeuroImage 184(Neurophotonics 2 2015), 171-179. https://dx.doi.org/10.1016/j.neuroimage.2018.09.025

Last edited 14 hours ago by David Boas
Meredith Pecukonis
Meredith Pecukonis (@meredith)
13 hours ago

what are typical STDEV and AMP values for motion artifact identification? Do you use one or both?

David Boas
David Boas (@dboas)
Reply to  Meredith Pecukonis
4 hours ago

I like to use AMP and I would use 0.05 or something smaller. This is in OD units. Meryem prefers the STDEV units. I forget what she prefers… maybe it is a value of 3?
You can use both.
But you should play around with different values and see how it works in terms of identifying motion artifacts. Do this by having a simple processing stream that just converts Intensity to OD, then identifies motion artifacts…. and that is it! And then change the thresholds and see what impact it has on identifying the artifacts.

Meredith Pecukonis
Meredith Pecukonis (@meredith)
13 hours ago

helpful papers for motion correction methods in infants:

Behrendt, H. F., Firk, C., Nelson III, C. A., & Perdue, K. L. (2018). Motion correction for infant functional near-infrared spectroscopy with an application to live interaction data. Neurophotonics, 5(1), 015004.

Di Lorenzo, R., Pirazzoli, L., Blasi, A., Bulgarelli, C., Hakuno, Y., Minagawa, Y., & Brigadoi, S. (2019). Recommendations for motion correction of infant fNIRS data applicable to multiple data sets and acquisition systems. NeuroImage, 200, 511-527.

Jordan Borrell
Jordan Borrell (@jordanborrell)
13 hours ago

I can’t run the hmrR_MotionCorrectWavelet function. “error generated at line 21….The specified module could not be found.” I do have the Wavelet Toolbox installed. Any thoughts?

Meredith Pecukonis
Meredith Pecukonis (@meredith)
Reply to  Jordan Borrell
13 hours ago

I would suggest uninstalling and reinstalling wavelet toolbox. I had to do this after I downloaded Homer3 for some reason.

Jordan Borrell
Jordan Borrell (@jordanborrell)
Reply to  Meredith Pecukonis
12 hours ago

Okay, that did not work, but I believe I have it working now. I did two things: 1) I noticed that the pathway was pulling from a separate folder, not the Homer3 folder that I download from Github. Instead, it was trying to set a path to the Hupport code from Github, which I put in a separate folder. It couldn’t identify some file that it was trying to find. I don’t know if the download for Homer3 and the Hupport Toolbox are intermixed, but it seemed to want to identify the Hupport folder instead. I removed the pathways to the Hupport folder, and it seems to be working now. 2) Additionally, I refreshed the Homer3 files from Github, so that may have helped. It’s hard to say which was the correct fix, but this may help anyone else running into a similar issue.

David Boas
David Boas (@dboas)
Reply to  Jordan Borrell
3 hours ago

you always have to be careful when you have your path set to see mutliple toolboxes that could easily have functions with the same filenames that perform very different operations. This is why I never save my path to default load in matlab. I force myself to always set the path each time I run matlab to make sure I know exactly which directories are being accessed.

Meredith Pecukonis
Meredith Pecukonis (@meredith)
13 hours ago
Heather Kwan
Heather Kwan (@hkwan)
12 hours ago

Not sure if I’m just not seeing it, but I don’t see any short separation channels in the practice problem data set. This would mean we can’t run a short separation regression with this data?

David Boas
David Boas (@dboas)
Reply to  Heather Kwan
3 hours ago

that is correct… this is a problem set about motion artifacts not SS regression

Karla Holmboe
Karla Holmboe (@karlaholmboe)
12 hours ago

Could you remind me of the time tomorrow that you are available tomorrow to go over the results of today’s exercise? I would like to join. I think you said 10am EST, is that right?

Heather Kwan
Heather Kwan (@hkwan)
Reply to  Karla Holmboe
12 hours ago

I believe that is correct! With the same link that we regularly use.

Karla Holmboe
Karla Holmboe (@karlaholmboe)
Reply to  Heather Kwan
12 hours ago

Thanks!

admin
admin (@admin)
Admin
Reply to  Karla Holmboe
4 hours ago

yes, 10am ET