Hi peter and other SPM users,
I am going through same issue for DCM. But my experiment is different. I am not able to understand how would i change code(see below), for my experiment. I went through spm_get_ons.m and spm_dcm_estimate.m to figure this out. but wasnt successful.
DCM.U.dt = SPM.Sess.U(1).dt;
DCM.U.name = [SPM.Sess.U.name(1)];
DCM.U.u = [SPM.Sess.U(1).u(33:end,1)];
I saw one more post on this which stated https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1004&L=SPM&F=&S=&X=61A0FC0F022B49A505&Y=analysisthread%40gmail.com&P=580450
"The DCM.U.u field contains the inputs (i.e., input vectors and modulatory vectors resampled into microtime). Microtime is the number of bins each TR is split into, and is specified by defaults.stats.fmri.fmri_t. The offset is specified in spm_get_ons. See around line 238. Therefore, if you you are using a design that has been setup by SPM, you should index it exactly as shown in the code you listed below: SPM.Sess.U(k).u(33:end,1) and so on, where k = condition you are indexing."
BUT, I am still not able to figure out how i change those three lines for my experiment.
I am changing the SPM-DCM code for first time for my experiment and hence if anyone of you guys can give me feedback on this, it would be helpful.
Thanks in advance
Kushal
----- Original Message -----
From: "Peter Zeidman" <[log in to unmask]>
To: [log in to unmask]
Sent: Monday, April 15, 2013 10:17:00 AM
Subject: Re: [SPM] DCM - batch
Hi Carmen,
(I'm CC'ing the mailing list in case anyone else is following this question.)
Your models are different because the one produced using the batch editor has mean-centring switched on, and the one using the GUI does not. Not only will this change your DCM.U.u (changing the mean to zero), but it also alters the interpretation of your DCM results. See the previous message I have pasted below from Karl.
(I can't guarantee there are no other differences in your models, but that's the most obvious one!)
All the best,
Peter.
...
If you centre the input, it will have a mean of zero. This means that the modulating input will increase and decrease the extrinsic connectivity (A parameter); as opposed to just increasing it, if the input is always positive. The interpretation of the B parameter therefore changes in a subtle way, and becomes closer to a classical interaction.
I hope that this helps.
With very best wishes,
Karl
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
> On Behalf Of carmen
> Sent: 15 April 2013 09:29
> To: [log in to unmask]
> Subject: [SPM] DCM - batch
>
> Dear SPM-list,
> I still don’t understand what exactly DCM.U.u is and why the values
> differ between a DCM-model created by GUI and the same model created by
> the batch code. Probably resulting from the differences here, the
> values for DCM.Ep.A, DCM.Ep.B and DCM.Ep.C differ as well.
> This is the code I use (model with 4 VOIs and two conditions as input):
>
> load(fullfile('D:\fMRI\Cannabis\Auswertung_Cannabis\Drona_R30\DCM\DCM_3
> \GLM','SPM.mat'));
>
> load(fullfile('D:\fMRI\Cannabis\Auswertung_Cannabis\Drona_R30\DCM\DCM_3
> \GLM','VOI_Thalamus_R_1.mat'),'xY');
> DCM.xY(1) = xY;
> load(fullfile('D:\fMRI\Cannabis\Auswertung_Cannabis\Drona_R30\DCM\DCM_3
> \GLM','VOI_S2_R_1.mat'),'xY');
> DCM.xY(2) = xY;
> load(fullfile('D:\fMRI\Cannabis\Auswertung_Cannabis\Drona_R30\DCM\DCM_3
> \GLM','VOI_Amygdala_L_1.mat'),'xY');
> DCM.xY(3) = xY;
> load(fullfile('D:\fMRI\Cannabis\Auswertung_Cannabis\Drona_R30\DCM\DCM_3
> \GLM','VOI_Hippocampus_R_1.mat'),'xY');
> DCM.xY(4) = xY;
>
> DCM.n = length(DCM.xY);
> DCM.v = length(DCM.xY(1).u);
>
> DCM.Y.dt = SPM.xY.RT;
> DCM.Y.X0 = DCM.xY(1).X0;
> for i = 1:DCM.n
> DCM.Y.y(:,i) = DCM.xY(i).u;
> DCM.Y.name{i} = DCM.xY(i).name;
> end
>
> DCM.Y.Q = spm_Ce(ones(1,DCM.n)*DCM.v);
>
> DCM.U.dt = SPM.Sess.U(1).dt;
> DCM.U.name = cellstr([SPM.Sess.U(1).name, SPM.Sess.U(2).name]);
> DCM.U.u = [SPM.Sess.U(1).u(33:end,1) ...
> SPM.Sess.U(2).u(33:end,1)];
>
> DCM.delays = repmat(SPM.xY.RT,DCM.n,1);
> DCM.TE = 0.04;
>
> DCM.options.nonlinear = 0;
> DCM.options.two_state = 0;
> DCM.options.stochastic = 0;
> DCM.options.nograph = 1;
>
> DCM.a = [1 0 0 0 ; 1 1 0 0 ; 1 1 1 0 ; 0 0 1 1 ];
> DCM.b = zeros(4,4,2); DCM.b(3,1,2) = 1; DCM.c = [1 0 ; 0 0; 0 0; 0
> 0DCM.d = zeros(4,4,0);
>
> save(fullfile('D:\fMRI\Cannabis\Auswertung_Cannabis\Drona_R30\DCM\DCM_3
> \GLM','DCM_Model1_batch.mat'),'DCM');
>
>
> Thanks a lot!!
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