run_preprocessing.sh — FreeSurfer-Based Intensity Normalisation¶

Location: BRC_structural_pipeline/scripts/run_preprocessing.sh
Authors: Ali-Reza Mohammadi-Nejad, Stamatios N Sotiropoulos
Last updated: 02 Oct 2018

Purpose¶

An alternative T1 intensity normalisation and brain extraction path that leverages FreeSurfer's autorecon1 step. Rather than relying solely on FSL FAST for bias correction, this script uses FreeSurfer's more robust pipeline (NU-correction and watershed-based skull stripping), converts the results back to NIfTI, registers them to native T1 space, and exports the output as T1_brain_norm.

This is used in the legacy --anatbasedFS path within FSL_anat.sh.

Processing Steps¶

1. Run FreeSurfer autorecon1¶

recon-all -i T1input -s FreeSurfer -autorecon1

Performs NU-intensity correction and talairach registration. Produces: - mri/T1.mgz — intensity-normalised T1 - mri/brainmask.mgz — brain mask

2. Convert to NIfTI¶

mri_convert -it mgz -ot nii mri/T1.mgz mri/T1_FS.nii.gz
mri_convert -it mgz -ot nii mri/brainmask.mgz mri/brainmask_FS.nii.gz

3. Register Back to Native T1 Space¶

flirt -ref T1input -in mri/T1_FS.nii.gz \
      -omat mri/rigid_manToFs.mat \
      -dof 12 -cost normmi -searchcost normmi

flirt -ref T1input -in mri/brainmask_FS.nii.gz \
      -out mri/brainmask.nii.gz \
      -init mri/rigid_manToFs.mat -applyxfm

Uses 12-DOF normalised mutual information registration to align FreeSurfer output back to native T1 coordinates.

4. Reorient to Standard¶

fslreorient2std mri/brainmask > mri/brainmask_orig2std.mat
fslreorient2std mri/brainmask mri/brainmask

5. Export Brain Norm¶

fslmaths mri/brainmask OutNormFolder/T1_brain_norm

Parameters¶

Parameter	Type	Description
`--workingdir`	Path	`processedT1Folder` — also used as FreeSurfer `SUBJECTS_DIR`
`--t1input`	File path	Raw T1 input image passed to `recon-all -i`
`--fsfoldername`	String	FreeSurfer subject name (`-s` flag)
`--outnorm`	Path	Output directory for `T1_brain_norm`
`--logfile`	Path	Log file path

Key Outputs¶

File	Description
`T1_brain_norm.nii.gz`	FreeSurfer-normalised brain mask, registered to native T1 space and reoriented
`<SUBJECTS_DIR>/FreeSurfer/mri/`	Full FreeSurfer `autorecon1` output (`T1.mgz`, `brainmask.mgz`, etc.)