| FREESURFER HANDS-ON WORKSHOP |
| Peggy Christidis | |
| November 18, 2004 | |
| National Institutes of Health |
| GOAL OF WORKSHOP |
| Start with several anatomical scans (MPRAGE) | |
| Create surface using FreeSurfer | |
| Overlay functional data on surface using SUMA (Hands-On class for SUMA on 11-19-04) |
| Agenda |
| FreeSurfer Flowchart |
| 1. Volume Preprocessing |
| Convert I.* files to BRIK using AFNI to3d | |
| Perform intensity normalization using AFNI 3dUniformize | |
| Register multiple volumes using AFNI 3dvolreg | |
| Average the registered volumes using AFNI 3dMean | |
| Convert to FreeSurfer format using FreeSurfer mri_convert |
| 1.
Volume Preprocessing Intensity normalization Ð critical for segmentation |
| 1. Volume Preprocessing |
| Convert I.* files to BRIK using AFNI to3d | |
| Perform intensity normalization using AFNI 3dUniformize | |
| Register multiple volumes using AFNI 3dvolreg | |
| Average the registered volumes using AFNI 3dMean | |
| Convert to FreeSurfer format using FreeSurfer mri_convert |
| 2. Segmentation |
| Intensity normalization | |
| Skull stripping | |
| White matter labeling |
| 2. Segmentation |
| Intensity normalization | |
| Skull stripping | |
| White matter labeling |
| 2. Segmentation |
| Intensity normalization | ||||
| Skull stripping | ||||
| Shrink-wrap algorithm | ||||
| Start with ellipsoidal template | ||||
| Minimize brain penetration and curvature | ||||
| White matter labeling | ||||
| Slide 11 |
| 2. Segmentation |
| Intensity normalization | ||||
| Skull stripping | ||||
| White Matter labeling | ||||
| Preliminary classification solely intensity based | ||||
| Relabeling of mislabeled voxels based on neighborhood information | ||||
| Define cutting planes | ||||
| Find connected components and fill | ||||
| 3. Tessellation and Inflation |
| Surface Tessellation | ||
| Use two triangles to represent each face separating white matter voxels from other voxels | ||
| Smooth initial tessellation with a deformable surface algorithm | ||
| Surface Inflation | ||
| Retain shape and metrics while making the interior of sulci visible | ||
| Slide 14 |
| 4. Manual editing |
| Examine surface for defects | |||
| manually reclassify voxels in the following areas: | |||
| Lateral ventricle | |||
| Fornix | |||
| Optic nerve | |||
| Basal ganglia | |||
| Other defect areas | |||
| Slide 16 |
| 8. Cutting and flattening |
| For a full surface patch | |
| For occipital patch |
| Slide 18 |
| SUMA (Hands-On class 11-19-04) |
| Convert surfaces to ASCII format | |||
| Align surface volume to experiment volume | |||
| Overlay functional data onto surface | |||
| Create link between AFNI and SUMA | |||
| View function on volume and surface simultaneously | |||
| Visit SUMA website for details: | |||
| http://afni.nimh.nih.gov/ssc/ziad/SUMA/ | |||
| Slide 20 |
| Acknowledgements |
| Alex Clark | |
| Bob Cox | |
| Richard Doucette | |
| Hauke Heekeren | |
| Shruti Japee | |
| Sean Marrett | |
| Rick Reynolds | |
| Ziad Saad | |