SPM8

Dear MarsBaRistas,

Are there any plans to make a MarsBaR version for SPM8?
It would be very appreciated,
merci,

Joyce!

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question on ReML estimation

Hi,
I am getting this error 

"?? Index exceeds matrix dimensions."

using the SPM ReML estimation
for fMRI designs, and I tried to use the alternative fmriStat as suggested in
the Marsbar faqs, but I still could not solve the problem.

 
The code is this:

1    des_path=spm_get('Files',filedir,'SPM.mat');
2    roi_files =
spm_get('Files',roidir,'*roi.mat');
3    des =
mardo(des_path);

4    forregion_number=1
5        roi =
maroi('load_cell', roi_files(region_number,:));
6        mY =
get_marsy(roi{:}, des, 'mean'); 
7        E =
estimate(des, mY);

8        mRes =
des_struct(E);
9        sY   = summary_data(mRes.marsY); 

Re: question on ReML estimation

Hi,

> "?? Index exceeds matrix dimensions."
>
> using the SPM ReML estimation
> for fMRI designs, and I tried to use the alternative fmriStat as suggested in
> the Marsbar faqs, but I still could not solve the problem.

Yes, that might be the SPM ReML failing to estimate the
autocovariance...  Or something else...

> 7        E =
> estimate(des, mY);
>
> 8        mRes =
> des_struct(E);
> 9        sY   = summary_data(mRes.marsY);

Line 8 gets the SPM structure from the estimated design, line 9 gets
the data that you have estimated on.  I can't now remember whether the
SPM structure includes a marsY, but in any case, the thing you are
trying to get with mRes.marsY is identical to to 'mY' - the data you
pass in for estimation on.

I presume that you wanted to estimate the autocovariance for each
region, then create a timecourse, with the autocovariance removed by
the estimated autocovariance filter.

For that you need to make sure that you are only extracting data for
one ROI at a time:

discrepancy of cluster size between Marsbar and SPM

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percent signal change for blocked-design fMRI

Hello,

I'm wondering if Marsbar allows for percent signal change to be extracted from
fMRI data collected using a blocked-design. Although I have not thoroughly
researched the Marsbar listserve, it seems that percent signal change in
Marsbar is only for event-related design. Is that correct or am I wrong?  I'd
like to confirm this before I try Marsbar with my data.
Thank you.

Sue

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iPhoneDevCamp as they present alongside digital heavyweights like Barbarian 
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Re: percent signal change for blocked-design fMRI

Hi,

> I'm wondering if Marsbar allows for percent signal change to be extracted from
> fMRI data collected using a blocked-design. Although I have not thoroughly
> researched the Marsbar listserve, it seems that percent signal change in
> Marsbar is only for event-related design. Is that correct or am I wrong?  I'd
> like to confirm this before I try Marsbar with my data.

It should be fine - in SPM an block design is just an event-related
design with long events.  You just need to specify the block (event)
length when calculating the signal change.

Best,

Matthew

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Help needed

I am trying to train my self to the marsBaR working on matlab 7.2 and  
spm 5, I think I got trapped into the "uigetfile" bug as none of the  
mat.file are found even if I downloaded the latest marsbar version.
I wonder if there is out there any pious user who could follow me in  
this training as I am in real need to become able to run roi analysis  
and statistics for my fMRI doctoral research.
Any help in how to proceed ( if procedure to de-bug remained the same  
etc) is extremely Welcome.

Thank you so much,

AKhairya

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