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Kohn, Nils | 7 Jul 16:06
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problem with get_marsy

Hi Matthew and all,

I'm trying to extract ROI data and get stuck rather early.. Since I'm rather new to sripting, this might
(hopefully) be an easy one..

after:
D  = mardo(spm_name);
R  = maroi(roi_file);
Y  = get_marsy(R,D,'mean');

I get: ??? Function 'get_marsy' is not defined for values of class 'mardo'.

I looked into D and R and got: 
D =

[mardo design object]

SPM working dir
Design type:            Unknown
Modality:               unknown
Has filter?:            N/A
Has images?:            unknown
MarsBaR estimated?:     no
Description:
Not specified

and 
D looks like this:
R{1}
(Continue reading)

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Binu Thomas | 8 Jul 17:47
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FIR timecourse

Hello Marsbar users,
                            I am trying the obtain the FIR time course from a design created in SPM5 and ROI's I have drawn in Marsbar, but I
get the following error:

??? Undefined function or method 'spm_get' for input arguments of type 'char'.

Error in ==> mardo.mardo at 178
  fname  = spm_get('CPath', fname);

Error in ==> HRFdiff at 4
D  = mardo(spm_name);

Please let me know if anyone of you has come across this error and has a solution.  

Thanks,

Binu

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Matthew Brett | 8 Jul 18:15
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Re: FIR timecourse

Hi,

>                            I am trying the obtain the FIR time course from a design created in SPM5 and
ROI's I have drawn in Marsbar, but I get the following error:
>
> ??? Undefined function or method 'spm_get' for input arguments of type 'char'.

Is it possible that you did not start your script with:

>> marsbar('on');

?  That puts the right directories on your path, including the version
of spm_get.

Best,

Matthew

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Matthew Brett | 8 Jul 18:47
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Re: problem with get_marsy

Hi,

> I'm trying to extract ROI data and get stuck rather early.. Since I'm rather new to sripting, this might
(hopefully) be an easy one..
>
> after:
> D  = mardo(spm_name);
> R  = maroi(roi_file);
> Y  = get_marsy(R,D,'mean');

It looks as if roi_file might have been a cell array of names, length
1, that resulted in a cell array of ROIs, so 'get_marsy' didn't
realize that it was an ROI object instead of a cell array.

MarsBaR also didn't recognize your design (as SPM5, SPM2, etc).  Is
this SPM8 by any chance?

Best,

Matthew

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Matthew Brett | 8 Jul 18:57
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Re: problem with get_marsy

Hi,

> I'm working with SPM5. In the GUI everything works fine, Marsbar recognizes my SPM designs (same SPM.mat
as used here) and I'm able to extract timecourses..
> Could I somehow have made a mistake in handing over the correct path? Though it seems to work (since I got
error messages on my first attempt, but not now).

Yes - I suppose that could have been the problem - glad to hear it is
working now...

Best,

Matthew

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Kohn, Nils | 8 Jul 18:55
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Re: problem with get_marsy

Hi,
And thanks for the answer!
I'm working with SPM5. In the GUI everything works fine, Marsbar recognizes my SPM designs (same SPM.mat as
used here) and I'm able to extract timecourses..
Could I somehow have made a mistake in handing over the correct path? Though it seems to work (since I got
error messages on my first attempt, but not now).
Best, NIls

-----Ursprüngliche Nachricht-----
Von: Matthew Brett [mailto:matthew.brett <at> gmail.com] 
Gesendet: Mittwoch, 8. Juli 2009 18:47
An: Kohn, Nils
Cc: marsbar-users <at> lists.sourceforge.net
Betreff: Re: [Marsbar-users] problem with get_marsy

Hi,

> I'm trying to extract ROI data and get stuck rather early.. Since I'm rather new to sripting, this might
(hopefully) be an easy one..
>
> after:
> D  = mardo(spm_name);
> R  = maroi(roi_file);
> Y  = get_marsy(R,D,'mean');

It looks as if roi_file might have been a cell array of names, length
1, that resulted in a cell array of ROIs, so 'get_marsy' didn't
realize that it was an ROI object instead of a cell array.

MarsBaR also didn't recognize your design (as SPM5, SPM2, etc).  Is
(Continue reading)

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Audrey-Anne Dubé | 9 Jul 16:03
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publications

Dear Marsbar users,

Can you tell me what is the article(s) that constitute validation of the marsbar? Or some paper that have used this analysis?

Thank a lot!

--
Audrey-Anne

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Matthew Brett | 10 Jul 04:52
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SPM8 release for testing, new docs

Hi,

I've been busy making a new release that works with SPM8, clearing up
the tutorial and the documentation.

The new documentation is up on the website - the release is on sourceforge...

Feedback welcome as usual.

Best,

Matthew

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Matthew Brett | 11 Jul 02:25
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Re: publications

Hi,

> Can you tell me what is the article(s) that constitute validation of the
> marsbar? Or some paper that have used this analysis?

I'm afraid marsbar is a bit difficult to validate, just because what
it does it so simple that it's difficult to imagine a publication on
it.  There are some obvious checks in the code (for example that SPM
analysis gives the same result as a marsbar analysis for single
voxels).

I haven't been keeping track of the publications using marsbar, but
now I look, I see that a search for 'marsbar ROI' in
scholar.google.com gives something in the range of 18 pages of hits,
nearly all of which are articles using Marsbar.

Just for a citation, there's:

http://marsbar.sourceforge.net/about.html#citing-marsbar

Best,

Matthew

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Joshua Buckholtz | 14 Jul 09:28
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timecourse extraction for single trials

Dear Matthew and others,

We have a slow event-related task with 60 trials, divided into 3 conditions. We’ve had luck using Marsbar to extract, for each subject, timecourses for each condition. However, we’re also interested in extracting, for each subject, timecourses for each of the 60 single trials. In thinking about how to do this, we’ve had the idea of creating a design matrix with 60 predictors (i.e. each trial onset has its own vector), and using the following code to extract FIRs for each event.

% Get definitions of all events in model
[e_specs, e_names] = event_specs(E);
n_events = size(e_specs, 2);
% Bin size in seconds for FIR
bin_size = tr(E);
% Length of FIR in seconds
fir_length = 24;
% Number of FIR time bins to cover length of FIR
bin_no = fir_length / bin_size;
% Options - here 'single' FIR model, return estimated
opts = struct('single', 1, 'percent', 1);
% Return time courses for all events in fir_tc matrix
for e_s = 1:n_events
  fir_tc(:, e_s) = event_fitted_fir(E, e_specs(:,e_s), bin_size, ...
                                 bin_no, opts);
end
    
In your opinion(s), is this a valid means of obtaining our desired result?

Many thanks,
Josh
 
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