export ROI in another fomat than nifti

Hi,
I am using SPM 5 and marsbar to build ROIs. When I export them, I only
get them in .nii format, which I can not further process (i need an .img
and .hdr file). Is there a way to export them in another format or how
can I convert them?
Cheers,
Nicole

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ROIs work with one model but not another

Dear Marsbar Users-
I am trying to extract timecourses from a set of functionally defined  
ROIs using a batch process.  I am able to successfully extract data  
from one SPM model, but not from another.  The models call on the  
same functional data, but they define the trial types differently,  
i.e., one model (the one that works) has 6 conditions and the other  
(the one that doesn't work) has 10 conditions.  I get the following  
error when I try to extract data from the second model....

??? One or more output arguments not assigned during call to 'maroi/ 
getdata'.

Error in ==> /usr/local/matlab6.5/spm2/vanilla/toolbox/marsbar/ <at> maroi/ 
get_marsy.m
On line 76  ==>   [y vals vXYZ mat]  = getdata(o, VY);

Error in ==> /home/alison/matlab/progs/marsbar_batch_dm.m
On line 30  ==>      Y  = get_marsy(R, D, 'mean');

I would be grateful to anyone who might know why the same ROI would  
work with one model, but not with another.

Thanks!
-Alison

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Re: ROIs work with one model but not another

Hi,

> I am trying to extract timecourses from a set of functionally defined
> ROIs using a batch process.  I am able to successfully extract data
> from one SPM model, but not from another.  The models call on the
> same functional data, but they define the trial types differently,
> i.e., one model (the one that works) has 6 conditions and the other
> (the one that doesn't work) has 10 conditions.  I get the following
> error when I try to extract data from the second model....
>
> ??? One or more output arguments not assigned during call to 'maroi/
> getdata'.

Hmm - I am sorry, I really don't know how that could be so.  The only
thing that the data extraction uses from the model is the images, and
these will presumably be identical between the two models.  You could
check this with

VY1 = mardo('analysis1/SPM.mat');
VY2 = mardo('analysis2/SPM.mat');

and check that, for example, the scaling and file names are the same:

VY1(1).pinfo
VY2(1).pinfo

Sorry not to be more help - but let us know how you get on...

Best,

Single voxel data extraction

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Re: Single voxel data extraction

Hi,

> We are trying to create a program in our lab that extracts roi timecourses
> from raw data (spm realigned and normalized) without going through spm or
> marsbar.  The idea is for the program to extract voxel values directly from
> the matrix of the image file.  However, we figured that before setting this
> program loose, we would do single voxel tests and compare the output of the
> new program to the marsbar output for the same voxel in a single subject.
> Somehow, our results are not matching at all, and the highest correlation we
> have gotten is .65.  We are measuring our coordinates in mm, since the voxel
> size is different between the spm templates and our data, but it still seems
> like we are not getting our information from the same point.  Is there some
> reason that marsbar might be pulling the coordinate from a different space
> than that in the image file matrix?   Also, the results from our program are
> always in the thousands or tens of thousands, while the marsbar output is
> always only in the hundreds.  Is there some sort of scaling going on?

Yes, if you used the default marsbar data extraction, it uses the
images from the SPM design, and these have been scaled to have a grand
mean, for each session, of 100.  You should be able to get the raw raw
data by using the full options, and choosing not to get the scaling
from the SPM images....

Best,

Matthew

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raw_data: extract with or without a design?

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