Hello, experts,

I keep getting the same error messages about "Index exceeds matrix dimensions" when I ran prepare feature set. Could anybody help to me figure out what is wrong? Thank you very much in advance.
Xin

Warning: Mask has different dimensions to the image files. Resizing... 
> In prt_fs>load_masks at 281
  In prt_fs at 58
  In prt_ui_prepare_data>buildbutt_Callback at 399
  In gui_mainfcn at 96
  In prt_ui_prepare_data at 48
  In @(hObject,eventdata)prt_ui_prepare_data('buildbutt_Callback',hObject,eventdata,guidata(hObject)) 
Feature set 'SEAT_run1' not found in PRT.mat. Creating...
Index exceeds matrix dimensions.

Error in prt_init_fs (line 192)
                            PRT.fs(fid).id_mat(sample_range(scans),4) = cid;

Error in prt_fs (line 61)
[fid,PRT,tocomp] = prt_init_fs(PRT,in,mids,mask,precmask,headers);

Error in prt_ui_prepare_data>buildbutt_Callback (line 399)
prt_fs(PRT,input);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in prt_ui_prepare_data (line 48)
    gui_mainfcn(gui_State, varargin{:});

Error in
@(hObject,eventdata)prt_ui_prepare_data('buildbutt_Callback',hObject,eventdata,guidata(hObject))

 
Error while evaluating uicontrol Callback
____________________________________
From: PRoNTo users [[log in to unmask]] on behalf of Wang, Xin [[log in to unmask]]
Sent: Monday, January 11, 2016 1:50 PM
To: [log in to unmask]
Subject: Re: multiple runs in fMRI

Thank you very much for the quickly reply, Jessica. My current single SPM.mat modeling runs separately results in unselecting most of trials in PronTo. So you may need more tests for the option 1. I am trying the option 2 in the manual.

Xin

-----Original Message-----
From: PRoNTo users [mailto:[log in to unmask]] On Behalf Of Jessica Schrouff
Sent: Monday, January 11, 2016 1:43 PM
To: [log in to unmask]
Subject: Re: multiple runs in fMRI

Hi Xin,

You don't need to change your SPM.mat if you select all the images. In theory, PRoNTo will 'add' the columns to end up with only one column for all your scans. (Note: this functionality has not been extensively tested).

Yes, you are correct for the second option. That would also be pretty simple to do: just load the SPM in the workspace and create a copy with only the session of interest (something like: newSPM = SPM; newSPM.session = newSPM.session(1); SPM = newSPM; save('newfolder_session1/SPM.mat','SPM')), and repeat for each session.

Yes, PRoNTo can concatenate multiple modalities in the feature set.
Basically, either you concatenate them yourself in the data and design, or you concatenate at the feature set step. The results will be exactly the same.

HTH,
Best,
Jessica

On 1/11/2016 6:34 PM, Wang, Xin wrote:
> Thank you very much, Jessica.
> This is my understanding, please correct me if I am wrong.
> To enter all runs as one modality, I need a SPM.mat file including all runs in continuous time and select the images in the same sequence. My current SPM.mat separates runs into different set of columns, and given "0"s for other runs in the according raw. I need to combine them into one set of columns.
>
> To enter runs as separate modalities, I need a SPM.mat file for each run starting at time 0, and select the according image. I am doing in this way, because I read in the manual that PronTo can concatenate all these modalities into one in later steps. Is it true?
>
> If I understood correctly, which way is better? I don't need to separate runs, but SPM batch scripts usually model the runs separately before combining the task-related contrasts cross runs.
>
> Thank you again.
>
> Xin
> -----Original Message-----
> From: PRoNTo users [mailto:[log in to unmask]] On Behalf Of
> Jessica Schrouff
> Sent: Monday, January 11, 2016 1:08 PM
> To: [log in to unmask]
> Subject: Re: multiple runs in fMRI
>
> Hi Xin,
>
> PRoNTo assumes that each 'modality' has one SPM.mat. If you enter a multi-session SPM, it will concatenate all the sessions into one for that 'modality'.
>
> When you have a single SPM.mat for multiple sessions, you should enter all the scans into one PRoNTo 'modality' (simply by selecting them all, in temporally consecutive order). If you wish to keep those runs separate, then you should divide your SPM.mat (i.e. have one SPM.mat for each 'modality', with onsets starting at 0).
>
> HTH,
> Best,
> Jessica
>
> On 1/10/2016 1:13 AM, Xin Wang wrote:
>> Hello, PRONTO group,
>> I try to enter multiple runs of fMRI data, and a single SPM.mat file for all runs in each subject. When I review data, the following message appears for each subject.
>> ans =
>>
>> Design of subject 2, group 3, modality 2, exceeds time series
>>
>>
>> Corresponding events were discarded
>> The same scans are implied in different conditions They will be
>> discarded Review the data set for more information
>>
>> Similarly, most scans are not selected.
>>
>> I found an old post about entering runs as separate modalities. Do I need to enter the runs one by one?
>>
>> Thank you in advance.
>>
>> Xin
>
> ---
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