Re: [Marsbar-users] ROI voxel values

[Matthew B. <mat...@uc...>]

Hi,

> I would like 
> to extract the individual activated voxels values for a given ROI instead of 
> the mean. a) Does MarsBaR provide information regarding each voxel 
> constituting the ROI - voxel count, individual voxel values, and the x, 
> y, and z coordinates (talairach coordinates?)? 

It does in its data structures.  You can save the individual voxel
values out to a text file using the interface (in the -devel version),
but if you want all the information, you could do something like:

% Get roi
roi_name = 'my_roi.mat';
roi = maroi(roi_name);

% get SPM design (just to get image information)
spm_mat = 'SPM.mat';
spm_design = mardo(spm_mat);

% Extract data - see 'help get_marsy'
y = get_marsy(roi, spm_design, 'mean');

% to select the region for which we want data
% In this case there's only one region
region_no = 1;

% Help yourself to information
voxel_data = region_data(y, region_no);
voxel_data = voxel_data{1};
voxel_xyz  = xyz(y, region_no, 'mm');


> c) Also, after invoking the extract data (PET) routine from the ROI 
> definition option, I get an output which says 'Data extracted and saved to 
> variable Y in Y.mat' and a bunch of Y values. Could you please explain what 
> those values represent? (I ran this analysis on your example data set).

By the way, the code above will only work with the new '-devel' version
of marsbar - you are currently using the old stable version.

Y is a (number of timepoints) by (number of rois) matrix, where value
Y(i,j) is the mean of all the voxels in scan i that are within the ROI
number j.

I hope that's kind of clear,

Best,

Matthew