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

SLICER: Initial Experience at Dartmouth

Tara McHugh, M.A.

Robert Roth, Ph.D.

Brain Imaging Laboratory

Dartmouth Medical School / DHMC

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Comparison of BRAINS to SLICER Views

Brains SlicerOrthogonal view: yes yesMax size of single plane: ¾ screen ~½ screenSize and plane interaction: not great planes individualizedCrosshair and planes interaction: yes noVariable center view of zoom: yes no

BRAINS SLICER

National Alliance for Medical Image Computing http://na-mic.org


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


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.


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?).


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. 2005

5 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


Functional MRI Data

2-back Working Memory Task in a Healthy Older Adult

SPM99 SLICER


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 designEvent-related designHybrid

SLICER may benefit from the following:


Documents

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