Dear Ezgi
The field DCM.d is missing. This specifies non-linear connections between regions. Even though you are not using this, the field still needs to be specified. Please add the following line to your script:
DCM.d = zeros(4,4,0);
Let me know if the problem persists.
Best
Peter
From: ezgi arikan [mailto:[log in to unmask]]
Sent: 02 August 2018 10:08
To: Zeidman, Peter <[log in to unmask]>
Cc: [log in to unmask]
Subject: Re: [SPM] PEB for DCM
Dear Peter,
Thank you very much for your help. I am attaching the script I used to create the DCMs. In the PEB analysis, as you pointed out, I didn't use estimated DCMs.
Best
Ezgi
On Thu, Aug 2, 2018 at 10:43 AM, Zeidman, Peter <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Ezgi
This is a generic error message, triggered when the fields (a,b,c,d) or priors are mis-specified in a DCM. I know there was an issue recently with resting state (CSD) DCMs. Perhaps you could share one of your DCMs, or the script you used to create it?
Best
Peter
From: ezgi arikan [mailto:[log in to unmask]<mailto:[log in to unmask]>]
Sent: 02 August 2018 07:59
To: Zeidman, Peter <[log in to unmask]<mailto:[log in to unmask]>>
Cc: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [SPM] PEB for DCM
Dear Peter,
I now receive the following error with the script I have used:
'??? Undefined function or variable "pC".
Error in ==> spm_find_pC at 52
if isstruct(pC)
Error in ==> spm_dcm_bmr at 91
[i,rC,rE,Np] = spm_find_pC(DCM);
Error in ==> spm_dcm_bmr at 68
[p,q,r] = spm_dcm_bmr(P(i,:),field);
Error in ==> dcm_peb_movement_modelled3 at 48
GCM = spm_dcm_bmr(GCM);'
Best Regards,
Ezgi
On Tue, Jul 31, 2018 at 12:15 PM, ezgi arikan <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Peter,
Thank you very much for your help. I am attaching the script. The DCMs in this script are not estimated. The first column has the full model.
I tried the script once more before I send it to you, and magically, it is running now. I am not sure whether I would get an error message later...
I checked with the SPM12 version I used, and realized that in some of my attempts, I have used an older version. Now I am using the SPM12 version 4 (SPM 12 7219). So maybe, it might have to do with that?
Still, with the batch (according to the Wikibooks instructions), I get the following error:
"Running 'DCM estimation'
Failed 'DCM estimation'
Undefined function or variable 'pC'.
In file "C:\Users\user\Documents\MATLAB\spm12\spm_find_pC.m" (v7075), function "spm_find_pC" at line 52.
In file "C:\Users\user\Documents\MATLAB\spm12\config\spm_cfg_dcm_est.m" (v7153), function "spm_run_dcm_est" at line 336.
The following modules did not run:
Failed: DCM estimation"
Best Regards,
Ezgi
On Tue, Jul 31, 2018 at 11:36 AM, Zeidman, Peter <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Ezgi
For the PEB analysis, you simply need a cell array of estimated DCMs with one row per subject. The DCMs can be estimated before putting them into the cell array, or you can put un-estimated DCMs into a cell array and then estimate them using spm_dcm_fit. You never need to estimate the DCMs twice.
Let’s focus on the analysis using scripting rather than the batch, because it’s easier to share the code by email. I assume you have code similar to the first box on the Wikibooks page. What error do you get?
Best
Peter
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of ezgi arikan
Sent: 31 July 2018 10:14
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: [SPM] PEB for DCM
Dear SPM experts,
I have a question concerning PEB for DCM. I am following the instructions provided in the 'https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_(PEB)<https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_%28PEB%29>' link. In the second step (Assemble your DCMs in a group file (GCM_name.mat) and estimate them (if not done already)), I initially thought I should be collating un-estimated DCMs from each participant, and then estimate them. But when I do this, I get an error message 'The following modules didn't run: DCM estimation'. I tried this with both a script and via the user interface. However, when I took already estimated DCMs from each subject, it works. So my question is, should I use already estimated DCMs for the first level analysis, and estimate them -again- by collating them in a GCM file before moving on with the second level PEB?
Thanks very much in advance.
Best Regards,
Ezgi
On Tue, Jul 31, 2018 at 11:36 AM, Zeidman, Peter <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Ezgi
For the PEB analysis, you simply need a cell array of estimated DCMs with one row per subject. The DCMs can be estimated before putting them into the cell array, or you can put un-estimated DCMs into a cell array and then estimate them using spm_dcm_fit. You never need to estimate the DCMs twice.
Let’s focus on the analysis using scripting rather than the batch, because it’s easier to share the code by email. I assume you have code similar to the first box on the Wikibooks page. What error do you get?
Best
Peter
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of ezgi arikan
Sent: 31 July 2018 10:14
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: [SPM] PEB for DCM
Dear SPM experts,
I have a question concerning PEB for DCM. I am following the instructions provided in the 'https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_(PEB)' link. In the second step (Assemble your DCMs in a group file (GCM_name.mat) and estimate them (if not done already)), I initially thought I should be collating un-estimated DCMs from each participant, and then estimate them. But when I do this, I get an error message 'The following modules didn't run: DCM estimation'. I tried this with both a script and via the user interface. However, when I took already estimated DCMs from each subject, it works. So my question is, should I use already estimated DCMs for the first level analysis, and estimate them -again- by collating them in a GCM file before moving on with the second level PEB?
Thanks very much in advance.
Best Regards,
Ezgi
