DBP:Sylvain Doug visit Dartmouth Feb 22 2006

Attendees

• Sylvain Bouix
• Bob Roth
• Tara McHugh
• John West
• Andy Saykin

Agenda

1. data acquired in slicer 2.5 need to match my ROIs to the greyscale cases (in analyze format)
2. use slicer 2.6 new features for D2 and Draw (slightly different)
3. align images to the AC-PC plane (is this making a matrix?)
4. review EM Segmenting

Highlights:

• Troubleshooting of Analyze files orientation and mismatch with label maps.
  • Sylvain spent time looking at Slicer 2.5 & 2.6 versions to match Analyze files formatted in the BRAINS program to align SPGR files with ROIs. Changing the Scalar Type from "Short" to "Unsigned Char" helped.
• Training on the new functionalities of the draw modules.
  • Sylvain showed Bob & Tara keyboard commands to help accelerate tracing ROIs. In the BIL we will not use the new feature in Slicer 2.6 "D2".
• Training on the Realign Resample module for both ACPC and Hippocampus realignment.
  • Sylvain brought copies of Realignment procedure from BWH-PNL. We reviewed the ACPC plane alignment and tested Realign/Resample steps on the long axis of the hippocampus.
• Training on alignment, matrices, and resampling.
• Training on using EMAtlasBrainClassifier.
  • Sylvain demonstrated cutting out the brain on a SPGR scan on a linux machine in the lab. Discussion regarding amount of time and expertise needed to clean up the EM segmentation automated in Slicer.
• Discussion on file formats.
  • Discussed how to format SPGR scans for easy reading in Slicer. BIL will now use nii format.
• Tour of the new imaging facilities at Dartmouth.
• Demo of Brain software and Dartmouth manual tracing procedures.
  • Tara showed Sylvain how the BIL thresholds using BRAINS, and using this tool when calculating the volume for the individual ROIS, and the ICV for each case. Demonstrated the orthogonal rendering in BRAINS to show how the crosshairs are linked across all 3 planes.