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Bias correction ("m" prefix for mean, "b" prefix for individual fMRI files)

The "m" indicates the images were bias corrected, which (if the option is selected) is done in the SPM "unified" procedure that runs with the segmentation. SPM terms this creating "modulated" images, hence the letter m. Bias correction adjusts for major intensity differences across the fMRI images; I found in one dataset that one side was much darker than the other, which is why I added the option to correct. This darker/brighter is often seen in raw T1 images as brighter or darker spots.

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Smoothing

Sometimes smoothing results in corrupted files. If so, turning on VERBOSE will also check for corrupted files after fMRI smoothing, and re-run for the problem files. In the example below, most studies had a few corrupted files, which were fixed with a second pass (attempts to smooth only corrupted files).

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These are the fMRI Preprocessing steps. The options are set in the Analysis GUI, where the proprocessing is started. These fMRI steps following after T1 preprocessing in this order, with some steps skipped depending on options.

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See also Preprocessing.

Matlab file: cspm_analysis_fmri_preprocess