fMRI Pre-Processing
fMRI Anatomy Processing Structure
Alt text:
Flowchart titled “FMRI Anatomy Processing Structure.” A blue box labeled “Create 3D image (dcm2nii)” branches to two modules: “Homogeneity correction (in-house code)” and “Skull stripping (FSL).”
On the right, text reads “Module selection and ordering is user-selectable,” with arrows indicating that processing steps can be arranged by the user.
Anatomy File Structure
Subdirectories for each structural series (e.g. "t1sag_208sl")
fMRI Functional Processing Structure
Flowchart of an fMRI functional processing pipeline. The sequence begins with “k-space despiking (spiral acq only)” followed by “Create 4D image (EPI: dcm2nii, Spiral: matlab recon).” From there, branches lead to “Physio noise correction (RETROICOR),” “Slice-time correction (SPM),” and “Motion + field map correction (FSL topup + SPM).” Optional modules shown in green include “Physio noise correction (COMPCOR)” and “Motion correction (FSL mcflirt).” A legend indicates blue boxes are default steps and green boxes are other available modules. Text on the right notes that module selection and ordering are user-selectable.
Functional (run) File Structure
Subdirectories organized as '[TASK]/[run_##]/'
Functional (field map)
Field map data found by extracting func/fieldmaps/fm_[TASK]/dicom.tgz
