> I have a basic question. I am trying to create a binary mask for each of
> our individual subject brains. I want to specify particular coordinates and
> make them 0 and the rest 1s, assuming if I have a 2x3x5 matrix, I want to
> make say 1x1:2x1:4 all 1s and the rest zeros. I am not sure if this is even
> possible.

It's not possible via the user interface, but if you are using SPM5, then it 
should involve a little bit of simple coding.

P                = spm_select(1,'nifti');  % Select an image
Ni               = nifti(P);   % NIfTI handle for input image
No               = Ni;         % Copy header to output image
No.dat.fname     = 'mask.img'; % Output filename
No.dat.dtype     = 'UINT8'; % Only a binary image, so 8-bit shoud be fine
No.dat.scl_slope = 1/255;   % Scalefactor so that a value of 1 is saved as 255
No.dat.scl_inter = 0;             % Make sure the intercept is 0
No.descrip       = 'Binary Mask'; % Some info about the file

% The data to be written
mask            = ones(size(No.dat));
mask(1,1:2,1:4) = 0;

create(No);                 % Write the header
No.dat(:,:,:,:,:,:) = mask; % Write the data

Best regards,