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> I am trying to write a program in Matlab that processes a series of images > in Analyze format, and writes the output as Analyze images. While I could > create the .img files without any problems, I was having a harder time > creating the .hdr files. I decided to use SPM functions to help me for > this step. > > I do have SPM installed, and am trying to use its functions to help me > create the header file. I was able to run the following example: > > % The volume that I wish to output > Volume = zeros(30,30,30); > > Info.mat=[2 0 0 0; 0 2 0 0; 0 0 2 0; 0 0 0 1] > Info.fname = 'foobar.img'; > Info.dim = [30,30,30,2]; > > spm_write_vol(Info,Volume) > > However, I think I am doing something incorrectly, as I encounter the > following warnings multiple times. Is there something I should be doing > differently? > > Warning: Cant get default Analyze orientation - assuming flipped > > > In spm_flip_analyze_images at 9 Try running >> spm_defaults first. SPM allows a site to have their data stored as left-handed (most people, and the official Analyze orientation) or right-handed. The preference is saved in spm_defaults.m. In order to determine the site preference, the spm_defaults.m file must first be executed (normally done when you type spm). > Moreover, I'm confused by how to set up the affine transformation matrix. > I'm trying to set up spacing to be 2mm x 2mm x 2mm. However, the resulting > x spacing is -2. Why would this be occurring? The default is to have left-handed storage, whereas Neurologists prefer to view their co-ordinates as right-handed (e.g. the T&T atlas). The flip in the x direction is so that locations within the .img file (assumed to be left-handed storage) can be interpreted within a right-handed coordinate system. You may want to take a look at the spm_get_space.m routine for more information about how the transform could be generated. > > Also, could someone please explain the meaning of the of Info.dim? What is > the meaning of dim[3]? I managed to get this to work by trial error, but > would prefer to understand what is happening here. Do you mean dim[4]? In SPM2, this is the datatype. See spm_type for more information. dim[3] is simply the number of slices in the file. Best regards, -John