NITRC SPM for fNIRS toolbox Forum: help

Spatial file type in spm error

Tatiana Pillsbury — Fri, 01 Mar 2024 6:08:09 GMT

I used the procedure "Conversion of NIRx NIRScout data format to SPM-fNIRS data format" by using the .wl1 , .wl2 and .hdr files. And this worked for me but when click spatial and try to upload files it suggests I use a .csv file. I collected my data using nirs star/nirs lab and am now trying to process in spm. The raw data file folder doesn't have any csv files. It does have config.txt, probe_info.txt, .dat, .hdr, .mat, .avg, and more. Does anyone know which files I need to use for this step or what works. I keep getting an error.

RE: Read data errors

Daina Crafa — Fri, 19 May 2023 12:51:19 GMT

I am having the same problem. Did you find a solution?

Read data errors

camsan — Mon, 23 Jan 2023 15:33:33 GMT

Hi all,

I am trying to use the spm fnirs toolbox to analyze fNIRS data obtained with NIRSport2 but I am unable to read and convert the raw data. There is no specific procedure in the manual that shows how to convert NIRSport2 raw data.

I tried to use the procedure "Conversion of NIRx NIRScout data format to SPM-fNIRS data format" by using the .wl1 , .wl2 and .hdr files but I run into the following error:

Not enough input arguments.

Error in spm_fnirs_convert_ui (line 90)
if ~isfield(P.fname.raw, 'type')
Error in spm_fnirs>push_convert_Callback (line 58)
spm_fnirs_convert_ui;
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in spm_fnirs (line 25)
gui_mainfcn(gui_State, varargin{:});
Error in matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)spm_fnirs('push_convert_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

Has anyone experienced the same problem? Is there another way to convert the data?

Thank you,
Best,
Cam

RE: error results _ never end

Manuel Munoz — Wed, 16 Nov 2022 3:03:16 GMT

I also have the same issue, as others have reported before. I have tried several Matlab version (from 2014 to 2022), and different operating systems (MacOS and Windows) and the error persists. The only way I get to prevent the never end loop is running twice the estimation GLM parameter. However, the result I get after calculating the activation p values is a blank surface of the rendered brain, without any significant cortical activation value. Looking at the beta values, it seems that they are smaller than they should be, or at least when you multiply them by 5 or 10, for example, it results in a cortical activation figure closer to that represented in the manual, but still not the same.

I wonder if someone found a solution to this issue. Any help would be much appreciated.

Best wishes,

Manuel

RE: error results _ never end

yasunori — Tue, 01 Nov 2022 2:10:23 GMT

I am also having the same issue.

When I stopped it, the command line showed the following error.

Operation terminated by user during spm_ECdensity

In spm_P_RF (line 63)
EC = spm_ECdensity(STAT,Z,df);
In spm_uc_RF (line 37)
[P, P, p] = spm_P_RF(1,0,u,df,STAT,R,n);
In spm_uc (line 31)
u = spm_uc_RF(a,df,STAT,R,n);
In spm_fnirs_viewer_stat>push_activation_Callback (line 211)
u = spm_uc(u,df, SPM.xCon(ic).STAT , SPM.xVol.R{view},1,SPM.xVol.S{view});
In gui_mainfcn (line 95)
feval(varargin{:});
In spm_fnirs_viewer_stat (line 35)
gui_mainfcn(gui_State, varargin{:});
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)spm_fnirs_viewer_stat('push_activation_Callback',hObject,eventdata,guidata(hObject))
Interrupt while evaluating UIControl Callback.

It seems that the program can not exit the following "while loop" of spm_uc_RF (line 37)

%-Approximate estimate using E{m}
%--------------------------------------------------------------------------
d = 1;
while abs(d) > 1e-6
[P, P, p] = spm_P_RF(1,0,u,df,STAT,R,n);
[P, P, q] = spm_P_RF(1,0,u + du,df,STAT,R,n);
d = (a - p)/((q - p)/du);
u = u + d;
if isinf(u), u=+Inf; return; end
end

I was using the sample data following the manual with Matlab R2022b on Mac.

Does somebody find any solution?

How to add covariates to paired sample t-test design?

Miranda Ramirez — Wed, 10 Aug 2022 17:15:35 GMT

Hello all

I have a within subjects design, and I want to examine a covariate of interest. Each subject had two maps generated (wins > control and nowins > control). These are my two con maps going into the second level as a paired t-test (wins>control > nowins>control). I want to see how learning rate (covariate of interest) scales with this comparison, but I'm confused on how to enter the covariate and what the contrast vector should be.

Should there be two vectors for the covariate values, one for the con_0001 and one for con_0002, or should they be in the same vector?

I only have one learning rate per subject, so should this learning rate value be duplicated (0.5 0.5 per subject) or with zeros separating (0.5 0 per subject)?

What should the contrast vector look like? My guess with how my design is currently set up, it would be .5 -.5 .5 -.5.

I attached a screenshot of the design matrix in case my description was not clear.

Thanks!

Association between ASL (repeated measure) & baseline covariate (paired t-test)

Nathalie Rieser — Tue, 10 May 2022 12:45:55 GMT

Dear all,

We are analysing ASL-data and our research question is, whether there is an association between a baseline value (one value per subject) and changes in ASL-signal (between 2 conditions, within one subject).
This means that every subject has one baseline value and two following ASL-scans (control vs. intervention) and we'd like to find out whether there's an association between these measures.
We used a 2-repeated measure design and compared the ASL scans in a paired t-test.

We wanted to ask, whether it is valid to look at the association between these measures within SPM in a paired t-test and if not, what the best way would be to do this.

Thanks a lot for your help,
Nathalie

Converting Raw Data to hemoglobin concentrations

Jana Welkerling — Mon, 09 May 2022 14:08:21 GMT

Dear all,

I am trying to convert my Raw Data from an fNIRS measurement with NIRSport to hemoglobin concentrations.

I read in the data with the function spm_fnirs_read_nirscout(F) which stores the results in a NIRS.mat file. Afterwards I am specifying all my features P which are needed for the convert function spm_fnirs_convert_ui(F{1},P), which calculates the hemoglobin changes by the Beer-Lambert Law.

load NIRS.mat
P.wav = [760 850];% wavelengths [nm] of the *.wl1 and *.wl2 files, respectively eg, 760 850 nm
P.age = [21] ; % age of subject [years] to be used in estimation of DPF
P.d = [3];% distance between source and detector [cm] eg, 2.5
P.acoef = [1.4033 3.8547; 2.6694 1.8096];%molar absorption coefficients [mM^-1cm^-1] of HbO and HbR at wavelength 1 and wavelength2.
P.dpf = [[6.658 5.5957]]; %DPF at wavelength 1 and wavelength
spm_fnirs_convert_ui(F{1}, P);

I do not get any error message, but regarding the new NIRS.mat file all fields are empty (od, hbo, hbr, hbt). So it seems like Matlab doesn't calculate anything.

Having a closer look at the function, I saw that I don't have the variable P.base.
All mentioned P.variables in the head of the function spm_fnirs_convert_ui(F{1}, P);
% P.wav light wavelengths
% P.fs sampling frequency
% P.nch number of channels
% P.ns number of samples
% P.mask mask of measurements
% P.fname names of raw files and converted file (NIRS.mat)
%
% P.d distance between source and detector
% P.acoef molar absorption coefficients [1/(mM*cm)]
% P.dpf differential pathlength factor [unitless]
% P.base baseline period [scan]

Can someone help me out what P.base might be and how I can specify it? And why is spm_fnirs not giving an error? By using the GUI of spm_fnirs the values of hbo etc. aren't empty when entereing the same features as mentioned above.

Happy to hearing from someone of you!
Thanks in advance

RE: Parametric modulation of regressors

marsarius — Thu, 21 Apr 2022 10:29:23 GMT

Never mind, I found a way

Parametric modulation of regressors

marsarius — Thu, 14 Apr 2022 11:26:15 GMT

Hello:

To my knowledge, there is no available routine to insert parametric modulators in the design matrix.
Since SPM-fNIRS utilities are to a large extent a repurposing of the SPM algorithms, it would seem that implementing parametric modulators should not be cumbersome.

Could you kindly provide a code snippet to implement parametric modulation or at least indicate what should I change in the code (in the function spm_fnirs_specify1st_ui.m) ?

Best wishes,

Mario