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Flag for running pipeline with no Global signal regressions #10

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b3n3dikt opened this issue Jul 13, 2020 · 0 comments
Open

Flag for running pipeline with no Global signal regressions #10

b3n3dikt opened this issue Jul 13, 2020 · 0 comments
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enhancement New feature or request

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@b3n3dikt
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Would be nice to have a flag to run the pipeline without global signal regression. The pipeline would run with GSR by default but if you turn on the flag it runs it without GSR. This would involve changing the docker run pipeline commands, as well as making edits to the dcan_signal_processing.m code in dcan boldproc.

change line 87 of this code to not include the WB:
dcan_bold_processing/matlab_code/dcan_signal_processing.m
This is line 87 changed to not run GSR: R = conc_noGSR(wm, vent, FR); %Running without GSR

And then one would also need to change the file it calls to have the correct dims by changing this file:
/dcan_bold_processing/matlab_code/hcp_matlab/conc.m
to something like this

function R=conc_noGSR(wm, vent, FR)
%% function R=conc(wm, vent, FR)
%
% This function concatenate and detrend regressors. It adds derivatives to
% wm, vent and WB
%% 
sR=[wm vent]; %simple regressors
dR=diff(sR);
dR=[0 0;dR];
R=[sR dR FR];
% R=detrend(R);

Ideally it would save a file with and without GSR if this flag is on, but just turning off GSR would be a great change as is :)

@b3n3dikt b3n3dikt added the enhancement New feature or request label Jul 13, 2020
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