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 | |