Full morphological processing of a T1 anatomical image using FreeSurfer's recon-all script [Dale et al. 1999], including integration of the additional Brainstem Substructures module. This module uses a Bayesian segmentation algorithm to segment four further brainstem regions in addition to the volumetric processing undergone in the standard FreeSurfer pipeline. More information can be found here.
The workflow includes:
- Image pre-processing: bias field correction, skull-stripping.
- Automated whole-brain tissue segmentation into CSF, cortical grey matter, subcortical grey matter, white matter, brainstem and cerebellum.
- Atlas-based full cortex parcellation and labeling using DKT40 scheme.
- Subcortical volumetry
- Cortical thickness computation for cortical regions.
- Optional full-head T2 or T2 FLAIR input to improve pial surface estimation.
- Automated segmentation of four additional brainstem structures: medulla oblongata, pons, midbrain and superior cerebellar peduncle.
- Comprehensive volumetric report including brainstem substructures.
Volumetric report output examples
Figure 1 - Freesurfer recon-all segmentation
Figure 2 - Brainstem substructures segmentation
Figure 3 - Volumetric information of brainstem substructures
Required inputs:
- T1
- Anatomical 3D image
- Isotropic resolution recommended
- Must be labeled as 'T1' modality
Optional inputs:
- T2
- Anatomical 3D image
- Isotropic resolution recommended
- Must be labeled as 'T2' modality
- T2 FLAIR
- Anatomical 3D image
- Isotropic resolution recommended
- Must be labeled as 'T2' modality and have a ‘flair’ tag
Minimum input requirements:
- Image must contain full skull (not brain extracted).
- For optimal results reliability, isotropic resolution is recommended.
- Recommended resolution: 1 mm isotropic.
- Minimum reliable resolution: 2 mm isotropic.
Outputs:
- Workflow main output:
- report.pdf: report file with results summary.
- Aseg_stats CSV files: Freesurfer volumetry and thickness complete results.
- Volumetric.csv: CSV file with gray matter parcellated regions volume and cortical thickness information
- Images in RECONALL step:
- T1.nii.gz: the input T1 image used in the tool.
- T1brain.nii.gz: preprocessed T1 image acpc-aligned.
- labeled.nii.gz: preprocessed and skull-stripped T1 image.
- tissueSegmentation.nii.gz: 5-tissue (csf, gm, wm, brainstem, cerebellum) tissue segmentation image.
- Folders:
- FREESURFER: Folder with full outputs of the FreeSurfer recon-all script [More information on FreeSurfer outputs].
- Brainstem Substructures output:
- T1.nii.gz
- brainstemSs_voxelspace.nii.gz
- brainstem_substructures_volume.csv
- FREESURFER output folder
Typical execution time:
- 8 hours.
References:
- FreeSurfer: [Dale et al. 1999], [Fischl et al. 1999], [Fischl et al. 2000], [Fischl et al. 2002], [Fischl et al. 2004]
- Brainstem Substructures: Iglesias et al. 2015
License Information:
- Users of this tool should be in possession of a FreeSurfer license. Obtaining a license is free and comes in the form of a license.txt file.
- More information on the FreeSurfer license can be found here.
- Follow this link to obtain a license key.