Local SPM code differences/changes Here is a somewhat complete discription of the changes in SPM code that are in place here. The changes are made in the following manner: The modified or new function files (.m) are placed in a directory created for this purpose (talk to Matt if you need further instructions). Since this directory occurs prior to the spm directory on the Matlab path, these function files will be read instead of the standard SPM files (using addpath in user's startup.m file). Thus, user or network specific changes can be made without disrupting the original SPM code. _noui.m files - No graphical interface These files are changed for many of the SPM functions and eliminates the graphical displays. This is especially useful for batch mode on a workstation where graphical output is not allowed, such as a telnet session. The elements with graphical tools are commented out of the code, and the status of a process is indicated in standard output rather than the SPM progress bar. To use the noui files in batch mode instead of the standard ones, batch mode should be started using spm_bch('filename.m','noui'). IMPORTANT: The output of these files should be carefully inspected, as the standard graphical output is not available. The preprocessing steps of realigning, coregistration (see next), and normalization should be examined graphically to ensure everything is ok. spm_checkcoreg.m - Graphical inspection of the coregistration process By typing this at a Matlab command prompt, the results of coregistration can be inspected graphically. The output is identical to the GUI output, but this is a tool to be used if the 'noui' option is used (see previous). This function can either be passed arguments (see help spm_checkcoreg) or a GUI if no arguments are passed. spm_slice_timing.m - Slice timing modifications This code allows the user to slice time correct for acquisitions in the coronal plane as well as the axial. It also allows it to be run in batch mode (see slicetiming.m batch file and corresponding addition to spm_bch.man). This has been tested for our standard coronal acquisition. The updated spm_write_plane.m must be included as well. spm_write_plane.m - Writes a plane in either coronal or axial directions. With an additional argument, a given slice will be written out as a coronal plane within a volume. spm_bch.m - Access the working directory from within a batch file. By adding thefollowing lines to the beginning of a variable description file,:. global working_dir disp(working_dir) files relative to work_dir defined in the analysis file can be used. This eliminates the need to have a variable description file for each subject and can use one file for multiple subject. See this file for an example. spm_vol_reorient.m - Reorients volumes similar to AIR This will mirror or rotate an actual volume rather than just changing the corresponding .mat file. This is necessary if using the old slice timing procedure. display_slices.m - Displays multiple slices of a volume with & without functional overlays In its current status, this code is modified to work only in batch mode. Matthew Brett's (MRC-CBU)original code was a GUI, but like a number of other things, I modified the code to be specific for our methods, but haven't had the chance to correct it entirely. See runover.m and over.m to see how this function is used. spm_fourresults.m - Four glass brains on a single page This will display four glass brains on a single page from either a single subject or multiple subjects. I found it to be most useful to show four brains of the same contrast of different subjects. It is a visualization technique rather than anything else. It will not provide statistics for the brains. spm_defaults.m - Defaults of SPM processing Since this file is located in the Matlab path eariler than the defaults for the enitre network, it will override those settings. Specifically, the most important difference is that our images are kept in neurological format (not mirrored) during normalization (they should be put in such format before any of the preprocessing).