fMRI Preprocessing Pipeline

Motion Correction

Slice-timing correction

Distortion Correction

Coregistration

Normalisation

fMRI PREPROCESSING PIPELINE

Smoothing

MRI PREPROCESSING PIPELINE

SPM

Freesurfer

Recon-all

- hippocampal_subfields_T1

Autorecon1

- Motion and intensity correction

- Intensity normalisation

- Skul strip

Autorecon2

- Automatic subcortical segmentation

Autorecon3

- Final surfaces

- Cortical parcellation

Hippocampal Subfields T1

REALIGN: spm_realign(Images, Flags)

RESLICE: spm_reslice(Images, Flags)

spm_slice_timing(Images, sliceorder, refslice, timing, prefix)

Realign & Unwarp

Coregister (Estimate & Reslice)

spm_coreg(VG, VF, Flags)

Normalise (Estimate & Write)

spm_smooth(Images, Q, S)