Using SPM.mat to Stay on Track (II)

Previously I discoursed at length upon the fatalistic nature of FMRI analysis, and how it leads to disorientation, depression, anxiety, and, finally, insanity. Those who are engaged in such a hopeless enterprise are easily identified by the voids that swirl like endless whorls within their eyes. I once knew a man driven out of his wits by just such an interminable cycle; he was found five days later on the sandy deserts of southern Indiana, ragged and filthy and babbling in alien tongues, scraping with pottery shards the boils that stippled his skin as though they had been painted on. Curse SPM, and die.

For those willing to prolong their agony, however, it is useful to know exactly what is contained within the SPM structure. Although not well-documented (if at all) on the SPM website, there are vast riches of information you can assay within the depths of the scripts themselves, which can be found in your spm8/spm5 library. (If they are in your path, you should be able to open them from anywhere; e.g., using a command such as "open spm_getSPM".) I have copied and pasted below the information from three such scripts, as well as a brief description about what they do. Good fortune to you.

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AFNI Command of the Week: 3dinfo

Researchers are always trying to find out more about their data. They examine at it from different angles; place it in their hand and feel its texture and test its heft; and look closely for portents and signs and the apocalypse.

3dinfo, similar to FSL's fslinfo and SPM's spm_vol, returns critical information about an FMRI dataset, such as the number of voxels along the x-, y-, and z-directions, the size of those voxels, and other header essentials, such as the number of volumes and the length of the repetition time (TR). This information is critical when performing steps such as slice timing correction with 3dTshift, when the researcher may want to know more about the number of slices and the acquisition of those slices, or when doing a step like cluster correction, where the voxel dimensions are a critical piece of information.

A few lesser known options include the -VERB option (in all caps), which generates even more information than the typical -verb option, and -echo_edu, which formats the standard output into a clear and easy-to-read table. This and more can be found in the following video: