Extract ROI data using command line

Hi All,

I am trying to figure out command line for extracting ROI data from 90 ROIs (full options), using an SPM
design with 72 time-points (3 runs x 24 images/run). 

When I complete this process in the GUI, these are the steps I follow:
1.  'Extract ROI data' (full options) > Select ROIs
2.  Use SPM design > Yes 
3.  Images from > SPM design
4. Scaling from > SPM design
5. Save output to .mat file

The resulting .mat file contains five variables, Y (72x90 double), Yvar(72x90 double), block_rows (1x3
cell), descrip (lists ROIs), info (1x1 struct), regions(1x90 cell), and sumfunc('mean').  

Would anyone be able to tell me exactly how to replicate this output using command line and/or a script?

Your help would be much appreciated.

Thanks in advance, 
Anna  
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Re: [SPM] Build Marsbar ROIs

Hi,

On Tue, Feb 7, 2012 at 4:55 PM, Anna Zamm <azamm <at> caregroup.org> wrote:
> Hi All,
> I would like to write a batch script that loops through a directory with 90 .img files and builds a marsbar
ROI (roi.mat) for each file.  I tried using maroi_image(filename) to do this, but Matlab gave me an error
message ('Undefined function or method 'spm_get' for input arguments of type 'char').   Any
suggestions on how to successfully batch this process would be much appreciated.
> Thanks in advance,

I think you want the marsbar mailing list for this one.

You may have omitted the line:

marsbar('on')

from your script.  This sets the paths correctly to run the rest of
the marsbar functions,

Best,

Matthew

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Import/Build ROI

What is the difference between building and ROI and importing one? Why are
there the two function with seemingly similar themes but very different
results?
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Re: loading an existing .nii file using maroi_image

This reminds me very much of a phone call down to Roy on the IT Crowd. I 
must have snipped that very critical line out of the script I was 
working from.

Thanks, turning on marsbar does, in fact, appear to be necessary for 
marsbar to function, and including the marsbar('on') line allows the 
script to run (at least as far as I've written it).

> >  ??? Warning: Struct field assignment overwrites a value with class "char".
> >    See MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As
> >  Structures Displays Warning for details.
> >    >  In maroi_image.maroi_image at 34
> >     In getcom at 29
> >  ??? Undefined function or method 'spm_get' for input arguments of type
> >  'char'.
>
> Did you try "marsbar('on')" at the beginning of your script?
>
> Best,
>
> Matthew

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2240 Campus Drive

loading an existing .nii file using maroi_image

Hi all,

I'm working on a utility script to enumerate all the clusters in an 
arbitrary .nii file (most likely binarised) and get the centers of mass 
and volume for each of them. It looks like marsbar has the necessary 
tools. Step one is loading the .nii file, which is where I am stuck:

     file_root='/path/to/file';
     thisvolfilename = 'filename.nii';
     vol_file = fullfile(file_root, thisvolfilename);
     fname=vol_file
     %load the volume
     IMG = maroi_image(fname);

executing the snippet (using real file names in a real filesystem):

fname =

/mnt/ldata/Seimens/language/crossmodal/ROIS/LFG.nii

??? Warning: Struct field assignment overwrites a value with class "char".
  See MATLAB 7.0.4 Release Notes, Assigning Nonstructure Variables As 
Structures Displays Warning for details.
 > In maroi_image.maroi_image at 34
   In getcom at 29
??? Undefined function or method 'spm_get' for input arguments of type 
'char'.

Error in ==> my_roifname at 22
roifname = spm_get('cpath', roifname);

I: ROI

>----Messaggio originale----
>Da: valentina-fin <at> libero.it
>Data: 25/01/2012 11.48
>A: <marsbar-users <at> lists.sourceforge.net>
>Ogg: ROI
>
>
>
>>
>>hello MarsBaR experts,
>>I'm writing you because I would need to ask your help on MarsBaR
>>I  want to knwn if it is possible extract one or more ROI made of a fixed 
>>volume of oriented parallelepiped (box) that is not necessary parallel to 
>>planes of image; each box must have voxel information that we have after co-
>>registration (i.e. we must keep analogous information). In detail  I want 
to 
>>select hyppocampus. Is it possible using MarsBaR?
>>Would you be so kind to give me some indication of where I can find this 
>>information please?
>>I would be very grateful if you could suggest me some articles or function 
>>that will help me in my research. Thank you very much.
>>Thank you very much for your time.
>>
>>
>>
>>Kind Regards
>>Valentina 
>>
>>

ROI

>
>hello MarsBaR experts,
>I'm writing you because I would need to ask your help on MarsBaR
>I  want to knwn if it is possible extract one or more ROI made of a fixed 
>volume of oriented parallelepiped (box) that is not necessary parallel to 
>planes of image; each box must have voxel information that we have after co-
>registration (i.e. we must keep analogous information). In detail  I want to 
>select hyppocampus. Is it possible using MarsBaR?
>Would you be so kind to give me some indication of where I can find this 
>information please?
>I would be very grateful if you could suggest me some articles or function 
>that will help me in my research. Thank you very much.
>Thank you very much for your time.
>
>Looking forward to hearing from you.
>
>Kind Regards
>Valentina 
>
>

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Help for extracting values using Marsbar

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importing binary masks in marsbar

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ROI

hello MarsBaR experts,
I'm writing you because I would need to ask your help on MarsBaR
I  want to knwn if it is possible extract one or more ROI made of a fixed 
volume of oriented parallelepiped (box) that is not necessary parallel to 
planes of image; each box must have voxel information that we have after co-
registration (i.e. we must keep analogous information). In detail  I want to 
select hyppocampus. Is it possible using MarsBaR?
Would you be so kind to give me some indication of where I can find this 
information please?
I would be very grateful if you could suggest me some articles or function 
that will help me in my research. Thank you very much.
Thank you very much for your time.

Looking forward to hearing from you.

Kind Regards
Valentina 

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import issues - help much appreciated!

Hello,

Hello, I made some native space ROIs in MriCron (NIFTI .img/.hdr files) and
imported them to marsbar (using the import function) in order to have
marsbar readable versions of said ROIs so that I could perform a signal
extraction from associated  beta images using marsbar. This all worked fine.
My results look great.

I would now like to calculate a ratio of average roi volume to wholebrain
volume for each of my subjects. I have a whole brain mask (NIFTI .img/.hdr)
which I would like to import into marsbar (effectively treating it as a
large ROI) in order to view the marsbar-calculated whole brain volume to
work out my ratio.

When I import said whole brain mask using the masrbar GUI or a script it
produces multiple wholebrain_n_roi.mat files (as little as ten or as many as
a couple of hundred! - either way, I was expecting a single
wholebrain_1_roi.mat file that relates accurately to the whole brain mask
(.img/.hdr) image that I imported). These individual files, when viewed in
marsbar, appear imcomplete in themselves and, while a vague approximation of
the mask I originally imported, are poor quality and many in number.

I'm a tad confused now. When I imported my individual subject ROIs the
output was just a single roi_1_roi.mat file for each subject as I expected.
These imported ROIs look fine when viewed in marsbar, although the ROI is
very small (~30mm3) so it's difficult to be absolutely sure that something
hasn't gone amiss here as well as when importing the whole brain masks.

I'm not sure what to do next. Any help appreciated!

Becky.
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