Main content

Home

Menu

Loading wiki pages...

View
Wiki Version:
Preprocessing fMRI Data: All data processing, analysis, and sharing will be done in accordance with the Organization for Human Brain Mapping’s (OHBM) best practices46. Functional imaging data will be processed and analyzed with FSL (FMRIB’s Software Library, www.fmrib.ox.ac.uk/fsl) using the standard processing stream from OpenfMRI (available here: https://github.com/poldrack/openfmri). BET will be used to extract the brain from the skull, and MCFLIRT will be used for motion correction. Participants will be excluded for movement greater than 3.0 mm in any direction. Individuals’ data will then be smoothed with a 6-mm full-width at half-maximum isotropic Gaussian filter. Confound motion parameter regressors will be created for TRs with a framewise displacement (FD) greater than 0.9. These FD-based motion regressors will be modeled along with the 6 motion parameters (from MCFLIRT), their squares, and the derivatives of each. A functional run for a subject will be excluded if more than 20% of all the volumes were tagged as high motion. Within-run parameters will be estimated at the first level using FILM, a fixed-effects model will estimate within-subject effects at the second level and group effects will be estimated using a mixed-effects model (FSL’s FLAME1) at the third level, which appropriately addresses the potential presence of differences in variance across groups. Spatial normalization will be performed using nonlinear registration with FSL’s FNIRT tool.
OSF does not support the use of Internet Explorer. For optimal performance, please switch to another browser.
Accept
This website relies on cookies to help provide a better user experience. By clicking Accept or continuing to use the site, you agree. For more information, see our Privacy Policy and information on cookie use.
Accept
×

Start managing your projects on the OSF today.

Free and easy to use, the Open Science Framework supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery.