Re: roi values

hello

you can get the milimetric value of the roi point. If your roi has been 
defined in a volume which is in
the MNI space then you'll get the coordinates in MNI space ...

roi_o = maroi('roiname.mat')
sp = native_space(roi_o);  %gives you the space of the image where the 
roi was define
Pos = voxpts(roi_o,sp);

Pos will contain the coordinate in pixel space.
to converte it in milimeter :

Posmm = sp.mat(1:3,1:3)*Pos + repmat(sp.mat(1:3,4),1,size(Pos,2));

I hope this help

Romain

Jac501 a écrit :
> Dear users,
>
> Sorry, I've serched the forum and can't find an obvious answer to this. 
>
>
> How do I extract roi x y z coordinates in MNI, or even better Tal space? I'm
> not interested in any stats, just cordinates for binary roi's to use with
> another program. At the moment I can on get centre of gravity from the .mat
> file. 

Re: Base space for ROI & Coordinate in millimeters

Hello,
I do not see a particular reason to save milimeters or image space 
coordinate. The important feature is to save
the volume dimention an orientation which were used to define the roi.
In this way you can get the roi in any other space. (and you can also 
the milimeter position)

roi_o = maroi('roiname.mat')
V = spm_vol('path_to_the_volume_you_want_to_put_the_roi_in')
sp = mars_space(V);
Pos = voxpts(roi_o,sp);

Pos will contain the coordinate in pixel space of the new image.

I hope this help

Jaime Shinsuke Ide a écrit :
>
> Dear all,
>
> I was confused about how the ROI’s are saved in Marsbar, but I think 
> now I got the point.
>
> They are saved in their native spaces.
>
> So, after loading the roiname.mat file:
>
> >> roi_obj = maroi(‘roiname.mat’)
>
> We can see it’s native space doing:

Marsbar doesn't recognize analyze images (spm5)

Dear Matthew, dear users,

i have a basic question on using Marsbar under spm5.
First, I couldn’t run Marsbar at all, then I downloaded spm5 files from
https://svn.sourceforge.net/svnroot/marsbar/trunk/marsbar/spm5/

Afterwards, I could run Marsbar, but I can not download binary images (in
analyze format) for creation of a VOI (option "import"). Specifically,
Marsbar seems to not recognize analyze images at all. Do I need to download
any other additional matlab files to resolve this problem? Sorry for such a
simple (stupid?) question – I, as a simple physician, have unfortunately no
idea from programming or matlab..
Thanks in advance.
Igor
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Re: Marsbar doesn't recognize analyze images (spm5)

Hi,

> i have a basic question on using Marsbar under spm5.
> First, I couldn't run Marsbar at all, then I downloaded spm5 files from
> https://svn.sourceforge.net/svnroot/marsbar/trunk/marsbar/spm5/

Hmm.  That doesn't sound like a good fix, but I don't know what
problems you had.  Was there an error message?

> Afterwards, I could run Marsbar, but I can not download binary images (in
> analyze format) for creation of a VOI (option "import"). Specifically,
> Marsbar seems to not recognize analyze images at all.

That's strange - are you selecting the .hdr files by any chance -
rather than the .img files?

How do you know that marsbar is not recognizing analyze images?

Best,

Matthew

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Re: ROI creation

Hi,

Sorry to be so slow to reply - both times...

> This question was posted at the beginning av this year, but I could not find
> the answer to it. I am trying to combine a pair of the marsbar AAL ROIs
> (specifically the fusiform and lingual gyri). I want to use it to compare
> these structures bilaterally. I also want to write the combination to an
> image such that I could use it for  analysis via small volume corrections
> within the ROI.
>
> Unfortunately, when I try to combine them I get...
>
> Warning: No volume resulted for ROI
>> In marsbar at 616
>   In marsbar at 1800
>   In marsbar at 485
>   In spm at 1276
>
> I have, however, been able to take a self generated functional ROI and
> combined it with a box ROI.

Is it possible that you have been using

r1 & r2

to combine the ROIs?  This gives you the voxels that are present in r1
_and_ in r2.  If you want voxels that are present in r1 _or_ r2, you
need:

Re: Marsbar doesn't recognize analyze images (spm5)

Hi, 

>> i have a basic question on using Marsbar under spm5. 
>> First, I couldn't run Marsbar at all, then I downloaded spm5 files from 
>> https://svn.sourceforge.net/svnroot/marsbar/trunk/marsbar/spm5/ 
> 
> Hmm. That doesn't sound like a good fix, but I don't know what 
> problems you had. Was there an error message? 

??? Error while evaluating uicontrol Callback. 

Warning: Name is nonexistent or not a directory:
C:\MATLAB6p5\work\spm5\toolbox\marsbar\spm5. 
  In C:\MATLAB6p5\toolbox\matlab\general\path.m at line 116 
  In C:\MATLAB6p5\toolbox\matlab\general\addpath.m at line 88 
  In C:\MATLAB6p5\work\spm5\toolbox\marsbar\marsbar.m at line 89 
  In C:\MATLAB6p5\work\spm5\toolbox\marsbar\marsbar.m at line 57 
  In C:\MATLAB6p5\work\spm5\spm.m at line 1502 
MarsBaR analysis functions prepended to path 
??? Undefined function or variable 'mars_veropts'. 

Error in ==> C:\MATLAB6p5\work\spm5\toolbox\marsbar\marsbar.m 
On line 93 ==> mars_veropts('defaults'); 

Error in ==> C:\MATLAB6p5\work\spm5\toolbox\marsbar\marsbar.m 
On line 57 ==> marsbar('on'); 

Error in ==> C:\MATLAB6p5\work\spm5\spm.m 
On line 1502 ==> evalin('base',xTB(i).prog); 

units for marsbar mean summary time course!

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Re: units for marsbar mean summary time course!

Hi,

> Can you kindly tell me what the units are for mean summary time course
> derived for a ROI?

The units are the usual SPM units, that is, change relative to a
baseline of 100, where 100 is the mean of the signal within the brain.
 Sorry, that's a bit brief, partly because the SPM units are a little
difficult to explain fully.

Best,

Matthew

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how to use the group analysis result as roi

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