Comparing contrats

Hi,

I am reading the marsbar devel tutorial. At the end of the tutorial, two contasts are compared (p.30,  "You
can see that the contrast value – which is proportional to the change in signal for a single event – is
greater for run 3 than for run 1"). My question is: how can I test if those two contrasts are significantly different?

I believe that one answer is to run a single model with run1 and run3 and test the contrast [1 -1] ([Run1
Run3]). 

However, if the ROI for run1 is different than the ROI for run3, how could I compare those two contrasts? In
this case, I wouldn't be able to compare them inside the same model (suppose I would like to test if left
amygadala activation is greater than right amygadala activation for a single patient).

A second unrelated question is: For answering the question "does area A on average activate more for
condition 1 than condition 2", marsbar calculates a new summary time course for each ROI and uses this time
course to estimate the model. Would it be correct to calculate the mean of the contrast values for every
voxel inside the ROI (calculated in spm con_*.img files) and use this value as an estimate of the average
activation in the ROI? How this procedure differs from marsbar method?

Thanks for your help,
Josue
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contrasts comparison

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Re: contrasts comparison

Hi,

> I am reading the marsbar devel tutorial. At the end of the tutorial, two
> contrasts are compared (p.30, "You can see that the contrast value – which
> is proportional to the change in signal for a single event – is greater for
> run 3 than for run 1"). My question is: how can I test if those two
> contrasts are significantly different?
>
> I believe that one answer is to run a single model with run1 and run3 and
> test the contrast [1 -1] ([Run1 Run3]).

Yes - that's right.

> However, if the ROI for run1 is different than the ROI for run3, how could I
> compare those two contrasts? In this case, I wouldn't be able to test them
> inside the same model (suppose I would like to test if left amygadala
> activation is greater than right amygadala activation for a single patient).

Well, for a single patient, that is a problem, because you'd expect
the variances and so on to be different between the two ROIs.  You
could get round this by creating a new time course for the two
sessions, two ROIs, in matlab for example (extract for session 1, save
to variable, extract to session 2, save to variable, concatenate, then
import data from Data menu.

Why are the ROIs different?  If you've selected the ROIs on the basis
of the activation for that session, you can easily run into problems
of bias.

> A second unrelated question is: For answering the question "does area A on
> average activate more for condition 1 than condition 2", marsbar calculates
> a new summary time course for each ROI and uses this time course to estimate
> the model. Would it be correct to calculate the mean of the contrast values
> for every voxel inside the ROI (calculated in spm con_*.img files) and use
> this value as an estimate of the average activation in the ROI? How this
> procedure differs from marsbar method?

It's very little different - it's only that, if you use marsbar for
the first level analyses, you can adapt the model correctly to the ROI
autocorrelation - but your suggestion is a reasonable shortcut...

Matthew

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Re: contrasts comparison

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Contrast Values- what are they exactly

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error with maroi

Dear marsbar users,

I tried to run a script in order to extract beta values and received the
following error message:

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

Error in ==> beta_script at 23
roi_array{1} = maroi(Kug_ROI_1);
----------------------------------------------

Can anybody give me a clue how to fix this?

Below you find the whole script.

Thanks in advance.

Regards, Tobias

-----------------------------------------
clear all;

cwd = 'F:\marsbar_ROIs';
cd (cwd);

dir{1} = 'F:\"subject folder"\SPM.mat';

roi_dir = ' F:\marsbar_ROIs';

Kug_ROI_1 = fullfile(roi_dir, 'hippo1_roi.mat');

roi_name{1}= 'hippo1';

roi_array{1} = maroi('load', Kug_ROI_1);

for vp = 1:length(dir)
    spm_name = dir{vp};

for i = 1:length(roi_array)
        roi = roi_array{i};

        D = mardo(spm_name);
        Y = get_marsy(roi, D, 'mean');
        E = estimate(D,Y);
        xCon = get_contrasts(D);
        E=set_contrasts(E, xCon);
        b = betas(E);

        marsS = compute_contrasts(E, 1:length(xCon));

        cont = marsS.con;
        Tval = marsS.stat;
        pval = marsS.P;
        pcorr = marsS.Pc;

        f = length(Tval);
        Roinr = zeros(1,f)'+i;

        connr=zeros(1,f)';
                for k = 1:length(connr)
            connr(k,1)=k;
        end

    fid = fopen(['VP',num2str(vp),'_Roi_',roi_name{i},'_ges_spss.txt'],'w');
    for j=1:length(Tval),
        fprintf(fid,'%3f %3f %3f %6.3f %6.3f %6.3f %6.3f\n', ...
        vp, Roinr(j), connr(j), cont(j), Tval(j), pval(j), pcorr(j));
    end
    fclose(fid);

end

end

----------------------------------------------
Tobias Melcher
Systems Neuroscience Unit
Department of Psychiatry and Psychotherapy
Georg-August-University Goettingen
von-Siebold-Str. 5
37075 Goettingen
Germany

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error with maroi

Dear Matthew Brett, dear marsbar users,

I tried to run a script in order to extract beta values and received the
following error message:

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

Error in ==> beta_script at 23
roi_array{1} = maroi(Kug_ROI_1);
----------------------------------------------

Can anybody give me a clue how to fix this?

The ROI was defined as a sphere.

Below you find the whole script.

Thanks in advance.

Kind regards,

Tobias

-----------------------------------------
clear all;

cwd = 'F:\marsbar_ROIs';
cd (cwd);

dir{1} = 'F:\"subject folder"\SPM.mat';

roi_dir = ' F:\marsbar_ROIs';

Kug_ROI_1 = fullfile(roi_dir, 'hippo1_roi.mat');

roi_name{1}= 'hippo1';

roi_array{1} = maroi(Kug_ROI_1);

for vp = 1:length(dir)
    spm_name = dir{vp};

for i = 1:length(roi_array)
        roi = roi_array{i};

        D = mardo(spm_name);
        Y = get_marsy(roi, D, 'mean');
        E = estimate(D,Y);
        xCon = get_contrasts(D);
        E=set_contrasts(E, xCon);
        b = betas(E);

        marsS = compute_contrasts(E, 1:length(xCon));

        cont = marsS.con;
        Tval = marsS.stat;
        pval = marsS.P;
        pcorr = marsS.Pc;

        f = length(Tval);
        Roinr = zeros(1,f)'+i;

        connr=zeros(1,f)';
                for k = 1:length(connr)
            connr(k,1)=k;
        end

    fid =
fopen(['VP',num2str(vp),'_Roi_',roi_name{i},'_ges_spss.txt'],'w'); for
j=1:length(Tval),
        fprintf(fid,'%3f %3f %3f %6.3f %6.3f %6.3f %6.3f\n', ...
        vp, Roinr(j), connr(j), cont(j), Tval(j), pval(j), pcorr(j));
    end
    fclose(fid);

end

end

----------------------------------------------
Tobias Melcher
Systems Neuroscience Unit
Department of Psychiatry and Psychotherapy
Georg-August-University Goettingen
von-Siebold-Str. 5
37075 Goettingen
Germany

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Percent signal change question

Hi,

I used marsbar to extract percent signal change values for all 4 
conditions of a block design experiment.
The experiment included 4 conditions, and all of them have been 
modelled, because there is no real
baseline condition in this experiment. ROIS have been defined as spheres 
around the maxima of the
RFX-activation clusters. Percent signal change values have been 
extracted for each subject and each condition.
These values have been averaged to give a group-percent-signal-change 
estimate for each experimental condition.
For some of the ROIs, all of these four values are negative, for other 
ROIs all of them are positive.
Now the question:
As I read in the marsbar documentation, all the values are scaled to the 
mean of the roi.
How can it be that the values do not sum to zero? The 4 conditions model 
the whole period of the experiment,
so I thought that they should sum to zero.

Best regards
Thomas Stephan

--

-- 
Dr. Thomas Stephan
Abteilung fuer funktionelle, strukturelle und molekulare Bildgebung
Zentrum fuer Sensomotorik
Klinikum Grosshadern der Universitaet Muenchen 
Marchioninistr. 23
81377 Muenchen

tstephan <at> nefo.med.uni-muenchen.de
+49 089 / 7095-4819 (Fon)
+49 089 / 7095-4801 (Fax)

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Re: Percent signal change question

Hi,

just to give a more intuitive explanation of the problem:
The Marsbar-FAQ tells me that the percent signal change is expressed in 
relation to the mean signal of the ROI.
But: When I look at all 4 conditions of the experiment, the mean of 
those 4 conditions signal changes should be the same
as the mean signal of the ROI, because there are no other periods in 
this experiment.
So how can they all be negative?
I think I still missed a detail with that?

Best regards
Thomas

Dr. Thomas Stephan
Abteilung fuer funktionelle, strukturelle und molekulare Bildgebung
Zentrum fuer Sensomotorik
Klinikum Grosshadern der Universitaet Muenchen 
Marchioninistr. 23
81377 Muenchen

tstephan <at> nefo.med.uni-muenchen.de
+49 089 / 7095-4819 (Fon)
+49 089 / 7095-4801 (Fax)

Thomas Stephan schrieb:
> Hi,
>
> I used marsbar to extract percent signal change values for all 4 
> conditions of a block design experiment.
> The experiment included 4 conditions, and all of them have been 
> modelled, because there is no real
> baseline condition in this experiment. ROIS have been defined as 
> spheres around the maxima of the
> RFX-activation clusters. Percent signal change values have been 
> extracted for each subject and each condition.
> These values have been averaged to give a group-percent-signal-change 
> estimate for each experimental condition.
> For some of the ROIs, all of these four values are negative, for other 
> ROIs all of them are positive.
> Now the question:
> As I read in the marsbar documentation, all the values are scaled to 
> the mean of the roi.
> How can it be that the values do not sum to zero? The 4 conditions 
> model the whole period of the experiment,
> so I thought that they should sum to zero.
>
> Best regards
> Thomas Stephan
>

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using conjunction activation to define ROI

Hi MarsBar users,

I'm new to Marsbar. I want to use the activation of conjunction analysis to
define ROI.
I used the procedure in the following way:

First I created a binary mask for the conjunction image in the way below:
               MarsBar--> Definition-->Build
                       -->Type of ROI -->image (selecting conjunction image)
                       --> maintain as binary mask?---Yes
                       --> apply function to image? ---> Yes
                       --> function to apply to image-->img > 0.0
                       --> description of ROI--> whatever I like
                       --> label for ROI--> whatever I like
                       --> save to whatever directory I want

Then combine this binary mask with whatever predefined MNI.roi in AAL together
as follows:
         MarsBar -> ROI definition-> Transform -> Combine ROI (r1 & r2) 
                            -->selecting conjunction image I just created and    
                        MNI.roi in AAL which I'm interested in, such as SFG_L  

                            --> Function to combine ROI: r1 & r2
                                             --> Description of ROI: eg.SFG_L
                                             --> Label of ROI: eg.SFG_L
                                             --> Save 

After that, MarsBar-> Definition->to view the combination. Using this to
determine a x,y, z coordinates to define my ROI. Should anyone tell me procedure
above is correct? if not, what should I do? 

Also, I found the combination is a range. Should I use the numbers of "centre of
mass" as x,y,z coordinates or pick up whatever numbers of the crosshair is
pointing (which is still in the range)? Thanks in advance!

Regards,

Chunhong

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