getting the coordinates of voxels in an ROI/ writing to an ROI

Dear users (and Matthew),

  I have two questions about things I'm having trouble with.

1) When you extract timecourse information for each voxel in an ROI using something like getdata.m, you get
a matrix with the data for each voxel in a separate column.  How can you retrieve the coordinates for the
voxel in each column so that you know which voxel each column refers to?

2) I'm trying to write values back to an roi, much like a user posted a question about a couple of months ago
(see below).  Essentially, we extract the data for all the timepoints in a roi, do some stats, and then want
to write back coefficient values for each voxel so that we can view/render them on a brain.  When I tried the
code Matthew suggested for the last user, the values that end up in the roi image are not the same ones I
entered (at least as indicated by the "display" function in SPM).  In fact, sometimes they aren't even the
same sign.  Any advice about what might be going on?  Does spm_write_vols do something to the values that I
don't know about?

  Thank you very much for your help!

Jana

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

	
Re: How to *write to* an image file at a given ROI?

by Matthew Brett Nov 14, 2007; 07:12am :

Hi,

>      But could someone please tell me how to *write* to a given ROI in the

resolution of ROI images

Dear Romain Valabregue and List,

I have a simple question: I'd like to create an ROI with a 1x1x1 mm resolution. 

I have tried following Romain's suggestion ("You can change it with the option 
(edit option) and 'choose base space for roi' just choose a volume with a 1x1x1 
resolution"; 
http://article.gmane.org/gmane.comp.graphics.spm.marsbar/588/match=resolution).

That is, I selected a normalized structural T1 (nifti) image of one of my 
subjects. But somehow marsbar / spm do not recognize this image "Unknown file 
format"), and now marsbar crashes whenever I want to start it (see error 
below). 

How can I create images with an alternative resolution than 2x2x2, and how can 
I get marsbar up and running again?

Thanks a lot for your help! 

Greetings, Rick 

MarsBaR analysis functions prepended to path
??? Error using ==> spm_vol>subfunc
/home/action/richel/Rick/data/fMRI/p01/structural/crop: Unknown file format.

Error in ==> spm_vol>subfunc1 at 83
    v = subfunc(P(i,:));

Error in ==> spm_vol>subfunc2 at 71
	V = subfunc1(P);

scripting marsbar with spm5 models

Hi,

it just took me some time to get my scripting working with severall subjects 
sharing the same model (spm5).

The critical code part is this: i is a variable eg i='VP_02'

    cd(['fMRI2/my_project/' i '/roi_analysis']);
    roi_model=mardo('/fMRI2/my_project/VP_01/ind_analysis_2/SPM.mat');
    P=spm_select('FPList','../nifti','^swf.*\.img');
    V=spm_vol(P);
    set_images(roi_model,V);

this didn't work because marsbar chose set_images for the @mardo_99/ directory 
instead of the @mardo_2 directory (there is no such file in the @mardo_5 
directory).

I did a workaround as: (using the source code of set_images in @mardo_2:
    D = des_struct(roi_model);
    D.xY.VY = V;
    D.xY.P = strvcat(V(:).fname);
    roi_model = des_struct(roi_model, D);

which seems to work.

Unless I totally missed something I would suggest to copy or link all 
functions not available in @mardo_5 from @mardo_2
Or is there something I overlooked?

Using marsbar 0.41, spm5 with the lates Updates and matlab 2007b.

Re: resolution of ROI images

Hi,

> That is, I selected a normalized structural T1 (nifti) image of one of my
> subjects. But somehow marsbar / spm do not recognize this image "Unknown file
> format"), and now marsbar crashes whenever I want to start it (see error
> below).

Oops, that's not a good feature!  It looks like you selected a file
without an extension that SPM can't load, but of course that shouldn't
crash on load.

If you saved the options, you might need to delete them again.  Try
finding a file called marsbarcfg.mat, probably in your working
directory, and deleting it.  If it's not there, try:

>> which('marsbarcfg.mat')

and deleting the file that matlab finds.

Best,

Matthew

-------------------------------------------------------------------------
Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!
Studies have shown that voting for your favorite open source project,
along with a healthy diet, reduces your potential for chronic lameness
and boredom. Vote Now at http://www.sourceforge.net/community/cca08

export image

-------------------------------------------------------------------------
Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!
Studies have shown that voting for your favorite open source project,
along with a healthy diet, reduces your potential for chronic lameness
and boredom. Vote Now at http://www.sourceforge.net/community/cca08

_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

how to proceed further with ROIs

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/

_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

nifti files

Does marsbar have any trouble reading spm5 nifti files?

-- 
J Labus, PhD

Adjunct Assistant Professor
University of California, Los Angeles

UCLA Center for Neurobiology of Stress
Connectivity and Computational Statistics Division 
Peter V. Ueberroth Building, Rm 2338C2
10945 LeConte Avenue
Los Angeles, CA 90095 

Phone:   (310) 206-0738
Fax:     (310) 825-1919
Campus mail code: 694907

email: jlabus <at> ucla.edu
website: www.cns.med.ucla.edu/Bios/LabusJ.htm

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/

Re: nifti files

Hi,

On Tue, Jul 22, 2008 at 8:31 PM, J Labus <jlabus <at> ucla.edu> wrote:
> Does marsbar have any trouble reading spm5 nifti files?

I don't think so, it uses the native SPM5 routines...

Best,

Matthew

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/

SPM model and marsbar FIR

Dear Matthew and all,

I'm new to this forum and I was wondering if the marsbar FIR time-course
estimation is based on a non-shape assumption even if the original
SPM-design was modeled with a canonical gamma HRF? So in other words, is the
time-course analysis dependent on the modelled HRF or is it a different
disentangeled analysis?

I would be very glad for a short comment!

Best regards,

Ruth
--

-- 
View this message in context: http://www.nabble.com/SPM-model-and-marsbar-FIR-tp18761085p18761085.html
Sent from the MarsBaR mailing list archive at Nabble.com.

-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/