importing ROI as cluster or as number labeled

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VOlumetric value for a given ROI

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Re: VOlumetric value for a given ROI

Hi,

> Does anyone know how I compute the volumetric for a given ROI?

If you use the view option with the ROI, the volume comes up on the
graphics screen when you select it.

Or:

>> roi = maroi('load', 'my_roi.mat')
>> volume(roi)

Best,

Matthew

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Marsbar SPM5

Hello all.

I'm attempting to run Marsbar with SPM5 and Matlab 7.4, without success.  

I have tried developmental versions 0.40 and 0.41.  

Upon selecting the toolbox in SPM, I receive no error message in Matlab. 
Instead, the toolbox is prepended to the Matlab path. 

The issue is that the GUI does not pop up.  Is there a command I'm not
invoking?  Or is compatibility at issue?

I kindly await any insight.

George Hana
--

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View this message in context: http://www.nabble.com/Marsbar-SPM5-tf3772792.html#a10667084
Sent from the MarsBaR mailing list archive at Nabble.com.

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Re: [SPM] Mean % Signal change over a box volume

Hi,

> I currently have a problem where I am trying to determine the mean
> percent signal change of the voxels within a  box shaped volume.  These
> voxels may or may not be above threshold in the statistical parametric
> map.  I can't find any way to do this in SPM5.  Generally speaking I can
> only get SPM5 to give information on one voxel at a time and never about
> a non-significant voxel.

You can get the raw data, and the mean of the data, using marsbar.
See: http://marsbar.sourceforge.net/

boxdef = struct('centre', [0 0 0], 'widths', [10 10 10]);
roi = maroi_box(boxdef);
D = mardo('SPM.mat');
y = getdata(roi, D);

That gets the data into a [number of images in design] x [number of
voxels in box] matrix.

Best,

Matthew

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%signal change over group

Hi,

I've done a first level group analysis with spm. Now, i want to know the % 
signal change in a particular ROI. When i use this function in marsbar, it 
asks for a event duration and later on, for which session it should be done 
(i've 6 sessions, because i have 6 patients) But i want the %signal change 
over ALL 6 of the sessions at once. Can this be done? Or should i just add the 
six up and then divide by 6?

Thanks in advance,

D. Bos

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Re: %signal change over group

Hi,

On 5/21/07, Daniel Bos <d_bos1985 <at> hotmail.com> wrote:
> Hi,
>
> I've done a first level group analysis with spm. Now, i want to know the %
> signal change in a particular ROI. When i use this function in marsbar, it
> asks for a event duration and later on, for which session it should be done
> (i've 6 sessions, because i have 6 patients) But i want the %signal change
> over ALL 6 of the sessions at once. Can this be done? Or should i just add the
> six up and then divide by 6?

You can create a combined event across sessions by adding all the
events from each session into one in the GUI for selecting events - or
there's a batch script template on the FAQ I think.

Best,

Matthew

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is masbar 0.41 useable?

Hello marsbar users,

I am an SPM5 user and so have installed v0.41 of marsbar.  With a little 
bit of stuffing around I have got it running, hower it will not let me 
set a design.  I have had no problem defining an ROI but when attempting 
to set the design i get these errors (show below) depending upon which 
method i attempt to use.

So my first question is, since this is listed as a development version 
of marsbar, is it actually usable?  Should I be reverting back to SPM2 
and marsbar 0.38?  If it is usable, has anyone else experienced these 
errors and the solution?

A quick note to the developers.  It is really really really annoying to 
have to navigate your directory structure every time you want to 
open/save a file.  It would be nice if marsbar would remember the last 
directory location used when opening/saving files.  Even better if it 
could use the Matlab interface which has the pulldown menu of recent paths.

Thanks in advance

Lee.

When trying to us 'FMRI models':

---------------

> >

??? Undefined function or variable 'mardo_5'.

Error in ==> mars_veropts at 23

  varargout = {mardo_5};

Error in ==> marsbar at 763

D = ui_build(mars_veropts('default_design'), des_type);

Error in ==> spm at 1604

evalin('base',CBs{v-1})

??? Error using ==> spm('PopUpCB',gcbo)

Undefined function or variable 'mardo_5'.

??? Error while evaluating uicontrol Callback

------------------

when trying to use 'Set design from file', error occurs after selecting 
SPM.mat:

----------------

??? Undefined function or method 'mardo_5' for input arguments of type 
'mardo'.

Error in ==> mardo.mardo at 215

    [o others] = mardo_5(o, others);

Error in ==> mars_arm_call>sf_check_design at 148

d = mardo(d);

Error in ==> mars_arm_call at 50

  [item_struct.data errf msg] = sf_check_design(item_struct.data);

Error in ==> marmoire.do_set at 113

  [tmp errf msg] = eval(item_struct.set_action);

Error in ==> marmoire.set_item_data_ui at 18

[o errf] = do_set(o, item, 'set_ui');

Error in ==> mars_arm at 29

  [o varargout{1}] = set_item_data_ui(o, varargin{:});

Error in ==> marsbar at 886

if mars_arm('set_ui', 'def_design'), return, end

Error in ==> spm at 1604

evalin('base',CBs{v-1})

??? Error using ==> spm('PopUpCB',gcbo)

Undefined function or method 'mardo_5' for input arguments of type 'mardo'.

??? Error while evaluating uicontrol Callback

---------------------

and when trying to 'Set design from estimated', again after I have 
selected an estimated SPM.mat:

-------------------

??? Undefined function or method 'mardo_5' for input arguments of type 
'mardo'.

Error in ==> mardo.mardo at 215

    [o others] = mardo_5(o, others);

Error in ==> mars_arm_call>sf_check_design at 148

d = mardo(d);

Error in ==> mars_arm_call at 124

  [data errf msg] = sf_check_design(data);

Error in ==> marmoire.do_set at 113

  [tmp errf msg] = eval(item_struct.set_action);

Error in ==> marmoire.get_item_data at 23

  [o errf] = do_set(o, item, 'set_ui');

Error in ==> mars_arm at 23

  [varargout{1} o varargout{2}] = get_item_data(o, varargin{:});

Error in ==> marsbar at 876

marsE = mars_arm('get', 'est_design');

Error in ==> spm at 1604

evalin('base',CBs{v-1})

??? Error using ==> spm('PopUpCB',gcbo)

Undefined function or method 'mardo_5' for input arguments of type 'mardo'.

??? Error while evaluating uicontrol Callback

------------------------

--

-- 
Lee Walsh
Prince of Wales Medical Research Institute
Sydney, Australia
Ph:  +61 2 9399 1014
Fax: +61 2 9399 1027
Email: Lee.Walsh <at> IEEE.org

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Re: Marsbar

Bill,

Lol.

I only had the base masbar directory set, I can't believe I missed that, 
it should have been the first thing I tried.  I've been having a few 
arguments with SPM lately and I was obviosuly blind with frustration >:(

Seems to be all working now and hopefully that's everything sorted.

Thanks a heap!

Lee.

Bill Budd wrote:
> Hi Lee
>  
> Just saw your message re marsbar and thought I'd say hello and try and 
> help before Matthew Brett gets out of bed. I dont use SPM5 so not sure 
> how to advise about the installation procedure for the version of 
> marsbar you are using but the error messages could be due to your 
> matlab paths not being setup properly. To test this just go to Set 
> Paths (under the "File" pull down menu in Matlab). Choose the 
> directory where youve installed marsbar and add with subdirectories. 
> Dont forget to save and try setting up a design again.
>  
> Hope this helps!
>  
>     -Bill
>  
> *_______________________________________________________*
>
> **
>
> **Bill Budd, PhD**
>
> *School** of **Psychology*
>
> *The **University of Newcastle*
>
> *Ourimbah** NSW 2258 **AUSTRALIA***
>
>  
>
> *Ph: +61 2 **4348* 4135**
>
> *Fax: +61 2 4348 4145*
>
> *Email: **Bill.Budd <at> newcastle.edu.au* <mailto:Bill.Budd <at> newcastle.edu.au>
>
> *_________________________________________________________*
>
>  

--

-- 
Lee Walsh
Prince of Wales Medical Research Institute
Sydney, Australia
Ph:  +61 2 9399 1014
Fax: +61 2 9399 1027
Email: Lee.Walsh <at> IEEE.org

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MarsBar and bounding box dimension

Hi,

does anyone know how MarsBar deals with images with different  
bounding box dimensions?

I have some PET data I've analysed in SPM99 which was normalised with  
a larger bounding box (dimensions 91 109 91). I want to use Marsbar  
to extract some unadjusted values for a connectivity analysis.

I notice that the MarsBar regions are displayed on a template with  
the larger dimensions, but I assume MarsBar expects images with a  
standard SPM dimension (79 95 68 in SPM 99).

Will the change in dimensions of the images cause problems in  
MarsBar? When I've tested this with single subject analyses using the  
same images with different dimensions I get different values, so I  
assume it does.

Is there a way of resetting the 'expectations' of MarsBar for the  
dimensions of the images?

Also, is there a way of displaying MarsBar ROIs on the actual data  
you will be using rather than the template to check if the two co- 
register.

Thanks,

Dave Sharp

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