SLICER: Initial Experience at Dartmouth Tara McHugh, M.A. Robert Roth, Ph.D. Brain Imaging Laboratory Dartmouth Medical School / DHMC NA-MIC National Alliance for Medical Image Computing

Comparison of BRAINS to SLICER Views BrainsSlicer Orthogonal view:yesyes Max size of single plane:¾ screen~½ screen Size and plane interaction:not greatplanes individualized Crosshair and planes interaction:yesno Variable center view of zoom:yesno BRAINS SLICER National Alliance for Medical Image Computing

Our current method is to partially trace in the Sagittal and Axial planes and then use the registered “telemarks” on coronal plane to trace the structure for volumetrics and shape analyses. Completing tracings in other planes can add too many telemarks to the Coronal plane, making it confusing. Partial Trace in Sagittal View on BRAINS SLICER may benefit from incorporation of a “partial tracing” feature. Make partial volume or traces without filling or creating opacity

National Alliance for Medical Image Computing Partial Traces in Sagittal View on BRAINS

Tracing in SLICER Traces in one plane are represented by a bar in other planes. This interferes with tracing in those other planes. A small dot or cross would facilitate tracing in multiple planes. The 3D diagram is required to understand location while moving through the brain. It would be helpful if each plane had a current slice number indicated. National Alliance for Medical Image Computing

Recommendations for ROI Tracing in SLICER Use arrow keys (more keyboard commands) (or need training on this). End Draw session from either the keyboard or mouse; not drag the mouse over to the Menu to click on “Apply” button. Edit mode – ability to move part of line without blacking it out. Line thickness should be very fine (easily select thickness). Skull stripping to involve only within the dura of the skull and end at the brainstem, without including the neck. Create the intracranial volume with minimal number of steps (3 – 5 steps from menu). Have volume batch into an excel sheet or other spreadsheet format. Thresholding: Need more training on this (only WM & GM?).

National Alliance for Medical Image Computing Tractography in Slicer Segmentation of the corpus callosum into 5 ROIs and generated tracts Healthy Older Adult Patient with AD C1-rostrum and genu, C2-anterior truncus, C3-middle truncus, C4-posterior truncus, C5-isthmus and splenium. Wang et al subregions of the corpus callosum.

Tractography in Slicer Eddy current correction Necessary for better quality data Option to investigate individual steps during processing Perform quality checks on individual processing steps Essential, especially for eddy current correction Integration of fiber tracking with fMRI e.g., pathway between 2 fMRI ROIs SLICER may benefit from the following improvements to DTI processing National Alliance for Medical Image Computing

Functional MRI Data 2-back Working Memory Task in a Healthy Older Adult SPM99 SLICER National Alliance for Medical Image Computing

fMRI in SLICER Low pass filter option is present but can’t be selected Batch processing of fMRI data once parameters have been selected Ability to analyze and display group data is essential Ability to display activations in normalized (template) space such as MNI and Talairach Simplify user interface option (general issue for SLICER) Add ability to check for artifacts and look for outliers in the functional data (group homogeneity) Create batch jobs for looking for artifacts Handle different design methods: Block design Event-related design Hybrid SLICER may benefit from the following: National Alliance for Medical Image Computing