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Pipeline: FSL_rsfMRI_AROMA
Type: BOLD
Description: FSL preprocessing of rsfMRI data with ICA-AROMA for automatic artifact removal
Source: NIACAL
External Link: FSL's software library
Details:
Crops the field of view of the T1 MPRAGE, extracts brain with BET with robust brain estimation. Then uses FEAT to discard the first two volumes, and does MCFLIRT motion correction and BET brain extraction of the functional image. Functional data are registered to the T1 cropped, brain extracted image with linear registration and BBR. FNIRT is used to apply Nonlinear registration between the subjects structural image and standard space (MNI152_T1_2mm brain). ICA-AROMA is then applied to the cropped, brain-extracted, normalized resting state scans to remove components automatically identified as movement. FAST is used to segment the T1 weighted image into gray matter, white matter (WM) and cerebrospinal fluid (CSF). Masks for WM and CSF are eroded then coregistered to the denoised functional data using FLIRT. These coregistered masks are then thresholded at 0.95, and the mean time series for each is calculated and regressed out of the functional data. A high pass filter of 0.01 Hz is applied, and the denoised functional data is warped to standard space. There is optional spatial smoothing.