For PET, E.R.fMRI and Blocked fMRI module, there is a check box called "Consider all voxels as brain" in "Create Datamat" window. If you select check for this check box, all of the voxels will be treated as "Brain Region".

Answers:

1. If you chose the default "Define brain region automatically", you did not treat all of the voxels as "Brain Region".
2. If you want to visualize the included voxels for a particular subject, you can click "Check image orientation" button in "Create Datamat" window.
3. There is no way to visualize them across participants, since we intersect the "Brain Region" on fly. However, I can provide you with a workaround below.

Workaround:

1. Run a quick Mean-Centering PLS (or any PLS) without perm/boot test (because we want do it quickly).
2. Load result file, and look for fields looks like *coord (e.g. st_coords in fMRI result) and *dim (e.g. st_dims in fMRI).
3. Type in the following commands (using st_coords & st_dims as example):

img=squeeze(zeros(st_dims));

img(st_coords)=1;

nii=make_nii(img);

view_nii(nii);

That is the way to visualize the included voxels across participants.

Thanks Jimmy - those commands worked perfectly! I tried saving this image as a .nii file and overlaying it on a template image in MRIcron, but the resulting .nii image was very very small (seemingly not in MNI space like the functional images are). Do you happen to know if there is any way to correct this so that I can overlay it properly?

One more word: Please don't get surprised if you find some of the brain voxels are out of the scalp boundary.

Because the subjects data are real data, and the template data is ideal data, there could be some discrepancies between these two.

However, if your template data was specially tailored and was only built from the selected subjects, all brain voxels should be inside the boundary.

The originator should be at least close to the middle of L-R direction. Therefore, dimension of [1405 2357 811] with originator of [27 38 18] is obviously wrong.

Please upload your template.nii and the original binary.nii that you obtained this morning to somewhere that I can have access (e.g. dropbox), and post the link here. I will look into it tomorrow, and post the detail script here.

I just took a quick look, and here's the answer:

1. When you use "make_nii.m", make sure that the 2nd argument is voxel_size and the 3rd argument is originator. In "FunctionalCoverageOrigin.nii", you obviously put originator into the 2nd argument. In order to get familiared with NIfTI and Analyze image data manipulation in detail, please visit:
   • http://research.baycrest.org/~jimmy/NIfTI
2. When I compare voxel_size between "FunctionalBrainCoverage.nii" and "ch2bet.nii", they are all [1 1 1]. Since their dimensions are different, one of them must be wrong. In order to use template image "ch2bet.nii" as reference, let's assume that "FunctionalBrainCoverage.nii" is wrong. Now, please use "view_nii" to open both, and switch both "Axes Unit" to "Millimeter". You have to manually compare the boundary of the brain region, and figure out the ratio between them. You will find that the coords displayed in [x y z] at crosshair for "ch2bet.nii" is about 2.7 larger than those for "FunctionalBrainCoverage.nii".
3. Download http://www.rotman-baycrest.on.ca/~jimmy/pad_nii.m, and save it into "plsgui" folder.
4. Now, run the following commands: (please copy them to your MATLAB command window, and they will work)

nii = load_nii('FunctionalBrainCoverage.nii');

nii=make_nii(nii.img, [2.7 2.7 2.7], [27 38 18]);

save_nii(nii,'binary.nii');

reslice_nii('binary.nii', 'binary2.nii', [1 1 1]);

b=load_nii('binary2.nii');

t=load_nii('ch2bet.nii');

b_org=b.hdr.hist.originator(1:3)

b_dim=b.hdr.dime.dim(2:4)

t_org=t.hdr.hist.originator(1:3)

t_dim=t.hdr.dime.dim(2:4)

% Since b_dim is smaller than t_dim, we have to pad it rather than clip it:

opt.pad_from_L=t_org(1)-b_org(1);

opt.pad_from_R=(t_dim(1)-t_org(1))-(b_dim(1)-b_org(1));

opt.pad_from_P=t_org(2)-b_org(2) ;

opt.pad_from_A=(t_dim(2)-t_org(2))-(b_dim(2)-b_org(2));

opt.pad_from_I=t_org(3)-b_org(3);

opt.pad_from_S=(t_dim(3)-t_org(3))-(b_dim(3)-b_org(3));

b2=pad_nii(b,opt);

save_nii(b2,'binary2.nii');  % if you overlay binary2.nii to template, they should match

% As a matter of fact, you don't need MRIcron, and you can view result immediately via "view_nii.m":

t.img(b2.img>0) = 255;

view_nii(t);