A Flywheel gear for running FSL's Processing Script: fsl_anat
Build context for a Flywheel Gear to execute FSL's fsl_anat.
This Gear performs the fsl_anat (Anatomical Processing Script) general general pipeline for processing anatomical images (e.g. T1-weighted scans).
Most of the pipeline involves standard use of FSL tools, but the bias-field correction has been substantially improved, especially for strong bias-fields typical of multi-coil arrays and high-field scanners.
The stages in the pipeline (in order) are:
reorient the images to the standard (MNI) orientation [fslreorient2std]
automatically crop the image [robustfov]
bias-field correction (RF/B1-inhomogeneity-correction) [FAST]
registration to standard space (linear and non-linear) [FLIRT and FNIRT]
brain-extraction [FNIRT-based or BET]
tissue-type segmentation [FAST]
subcortical structure segmentation [FIRST]
The overall run-time is heavily dependent on the resolution of the image but anything between 30 and 90 minutes would be typical.