NITRC Homer2 Forum: help

Splitting .nirs file into 2 separate files

nguyentienhn — Fri, 13 Sep 2019 13:04:13 GMT

Hello,

I am using Homer2 for an fNIRS analysis and am just wondering how to split a .nirs file into 2 separate .nirs files using MATLAB? I would like for the first half of the channels (Sources 1-8, Detectors 1-16) to go in one file and the other half in another file before I begin my analysis.
Thanks!

AtlasViewer Probe Fabrication Error: incorrect alignment

Rosalyn Hithersay — Mon, 27 Aug 2018 20:41:23 GMT

Hi there,

I'm trying to use the 'register atlas to head size' and 'probe fabrication error' tools in AtlasViewer but have run into a few problems. I'm using Homer2 V2_3 with Matlab R2016a.

Initially, I got the following error message:
[color=#ff0000]Reference to non-existent field 'AlAr'.[/color]

[color=#ff0000]Error in ellipse_1020_costfun (line 20)[/color]
[color=#ff0000]f = (HC-headSize.HC)^2 + (IzNz-headSize.IzNz)^2 + (AlAr-headSize.AlAr)^2;[/color]

[color=#ff0000]...[/color]

[color=#000000]I updated headSize.AlAr in ellipse_1020_costfun to headSize.LPARPA which seems to have fixed the register to head size problem.[/color]

[color=#000000]When I try to look at the probe fabrication error though, it seems to be missing out short-separation channels. I have digpts files from a group of participants for an array with 16 sources and 16 detectors, making 44 channels: 42 at 30mm and 2 at 10mm. However, I only get 30 sets of co-ordinates for the errors. I plotted the locations for the SD file and the group means from the 30 sets given, and it looks like for the SD file the short seps are there, but the last two detectors are missed off. For the group means form the digitised points, it looks like the detectors for the two short-sep channels are missing, but that then means that the order of the detectors is different from the SD file, making it look like there's a large placement error for some detectors.[/color]

[color=#000000]Is there a way to include all sources and detectors?[/color]

Thanks,

Ros

[color=#000000] [/color]

Possible bug in hmrMotionCorrectPCA

Frank Fishburn — Tue, 10 Jul 2018 20:02:21 GMT

Hello,

I am testing tPCA on some simulated data and am finding that nSV sometimes gets set to 0 when the first singular value is greater than nSV, resulting in no correction being applied. I don't think this is a common scenario, so it's probably not a major problem. However, it looks to me like the issue is on lines 67-70:

if nSV<1 & nSV>0
ev = diag(svsc < nSV);
nSV = find(diag(ev)==0,1)-1;
end

It looks to me like it can be fixed with this change:

if nSV<1 & nSV>0
nSV = find(svsc>=nSV,1,'first');
end

Hope this helps. Apologies if I missed something.

Best,
Frank

hmrMotionArtifactByChannel

Jessica Defenderfer — Fri, 29 Jun 2018 19:59:44 GMT

Hello, looking for some advice from experienced and knowledgeable NIRS scientists - I am working through some data obtained from the temporal and frontal regions on the left hemisphere (thirteen 30mm channels, one 10mm channel). I am becoming more aware of the potential unwanted effects/artifacts from the temporal muscle. I have a few questions about processing these data:

1) Is hmrDeconvHRF_DriftSS the only option for regressing short channel data from long channels? There seem to be a lot of other parameters built in to that one step that I don't think I need (i.e. convolution, temporal basis functions).

2) Since I feel that motion artifact may not be common across all channels in my probe design, I decided to try hmrMotionArtifactByChannel. From what I've read, this option will essentially do the same thing as hmrMotionArtifact, but identify artifact specific to each channel (not marking it on all other channels). So far, it doesn't appear to be working this way. For example, one participant has several ampthreshold violations on 2 channels, but in their procResults, none of the trials were accepted across all channels and conditions. I may be misunderstanding what I should expect, but my initial expectation was to see the number of accepted trials to be varied across channels and conditions.

3) I only have one short distance probe. Would it be effective to also run PCA in addition to regressing out the short probe? I realize that the scalp fluctuations may be different on other areas of the scalp.

Wavelet analysis issue in Homer2 toolbox

Geoff Green — Wed, 28 Feb 2018 23:45:10 GMT

I have a question about the wavelet analysis in Homer2, wanted to know how much experience you have had with it and if you'd be able to help with this issue. I have acquainted myself with the software in hope to apply wavelet analysis to the preprocessing stream instead of bandpass filtering.
Currently, I have been able to convert nirx data to .nirs files (homer2 compatible) in order to apply specific preprocessing functions to the time series for specific channels. There are 2 different wavelet corrections, motion correct wavelet and motion correct kurtosis, of which I am trying ti use as a substitute for a bandpass filter. I applied the kurtosis to the time series, but this affected the data in a strange way (image attached "conc_kurtwave") compared to what the data looked like before the kurtosis wavelet (image attached "conc"). Is the kurtosis suppose to have this strange oscillatory type of effect? I have read a little about it, and it seems to be an advancement on the regular wavelet analysis, regular motion correct wavelet sets one threshold value for the wavelet coefficient rejection (Molavi et. al, 2012), while the motion correct kurtosis wavelet has a threshold that varies as a function of the frequency of artifacts in the data; it is iterative (Chiarelli et. al, 2015).

I want to be able to compare this to the regular motion correct wavelet to see which renders a better hrf in the data, however, I get this error message (image attached) when i try to use the regular motion correct wavelet. I see no error in the script it is referring to. I just wanted to know if you had to go through this, or if you know of/can suggest any possible resolutions.
If there is anything that needs clarification, just let me know.
Best,
Geoff D. Green II

Errors for all actions

Patrick Hislop — Tue, 23 Jun 2015 14:12:39 GMT

I have an issue in Homer2 wherein any action I take will print out an error in the command area of matlab. I will list my setup procedure for Homer2 below.

-Download Homer2 zip and extract
-include homer2 folder and subfolders in paths
-go to the folder that contains my .nir data
-run Homer2_UI()
--OR--
-Download Homer2 zip and extract
-include homer2 folder and subfolders in paths
-include the folder that contains my .nir data
-run Homer2_UI()

both procedures produce the same result. An image with a sample of the errors is attached, and any help is appreciated.

Welcome to Help

David Boas — Fri, 03 Aug 2012 13:22:57 GMT

Welcome to Help