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FreeSurfer Tutorial: Applying FreeSurfer Tools to SPM fMRI Analysis

The purpose of these series of exercises is to give you some familiarity with integrating FreeSurfer and SPM's functional analysis. The main challenge in the integration is getting a subject's anatomical data properly registered with their functional data. Once registered, you can use FreeSurfer display tools to visualize your SPM functional activation maps on the subject's anatomical volume and on the surface.

For structural data, we will use ${SUBJECTS_DIR}/bert and ${SUBJECTS_DIR}/fsaverage. For functional data, we will use fbert.img. The functional data set consists of 85 volumes, each 64 x 64 x 35 voxels, with size 3.4375 x 3.4375 x 4.0 mm^3. TR = 3 sec. The experiment a periodic block design with 15 sec ON blocks of simultaneous finger tapping, flashing checker board, and auditory tone. The OFF blocks are rest periods. The paradigm starts with an OFF block. The functional analysis has been precomputed for this data by running Feat. Feat was set up using the Simple Model Setup, ABAB..., A = 15 sec, B = 15 sec; and a Full analysis was performed to create fbert.feat.

1.0 Registration

2.0 Overlaying

See also SPM and Freesurfer