Neurosurgery wishlist

1. Better editor

- "magic wand" like Photoshop to select nearby and *connected* pixels with similar intensity

- sensitivity controls for the levelset threshold thing

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2. Better segmentation

- EMSegmenter is nice, but it is time-consuming and too involved for basic things. Very often all I want is a basic but presentable rendering of a subject-specific cortex. As yet, there is no easy and quick way to do this. BrainLab and GE both have quick surface generation algorithms which work reasonably well based on one or a few intensity seed points.

3. Tool/UI requests

- Getting the crosshairs squared away and working right is CRUCIAL.

- need ability to measure angles and distances

4. Usability things

- I'm not sure exactly how, but would like to find a better way to move things around in 3D. The best I can think of so far is rotational motion along some sort of level set, either of a structural image, or a distance function from some pre-defined "central feature". Pushing a (arrow?) key would move in and out.. Maybe this would be less intuitive than the current method of "rotate plane" move, "rotate plane" move, etc... But maybe it would work?

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Need to merge the below dump:

- Change default Analyze format file load option to "center" (currently must do manually, else the image will be centered on a corner of the cube).

- "Go to Editor" option in Data module should bring up the *selected* dataset in the Editor. Currently, "Go to Editor" brings to the editor for the datatype (fiducial, transform, volume, etc) but the Editor displays the last used volume, so an extra step is required to get to the right data (this can be confusing for new users, and is generally frustrating). "Go to Editor" should tell the appropriate Editor which volume/list to display.

- improved interactive registration: two main points 1) allow movement of one volume against another with mouse and arrow keys. 2) add option to Transform module to change the overlay mode to something which allows better visual distinction between the overlay volumes (without having to change the individual display properties for both volumes).

- quick and easy segmentation of the cortical surface.. Most of the time we don't need a complicated segmentation, just a reasonable representation of the cortical surface. I got a forward of an email from Ron about EMSegmentSimple, but have not had a chance to try it yet -- but maybe this will work.

- improve the crosshairs functionality. The new crosshair with "Jump to slice" option enabled is GREAT, but the refresh is too slow to be used for precise placement (ie of seedpoints).

- Editor: magic wand, like photoshop. The levelset tool is nice for some applications, but can be difficult to use because it selects everything in the slice at a certain intensity. The magic wand would only select *connected* pixels at a certain intensity level (this would be very helpful for tumor segmentation in particular: often the tumor will have a similar intensity to skull, so the levelset tool grabs everything).

- Add simple ruler and angle measurement functionality. Distances can be taken between the first two fiducials in a list, but this is not a full solution. The ideal

- Editor: fix the eraser

- Editor: modify the threshold tool to allow thresholding only within a certain region (would be helpful for tumor segmentation).

- Editor: add option to select the labelmap to modify. At present, modifying a labelmap requires changing the labelmap in the slice viewer, which can be difficult for new users to grasp.

- Editor: make "Undo" work for Editor.

- Change the "Testing: (Tensor Estimation & Glyphs & Tractography Settings)" to apply the ThresholdMask by default.

- Add function to reflect fiducial positions between hemispheres across a user-defined AC-PC plane.

- Simple tool for labelmap duplication

- Fix the threshold buttons in Volume display:

- Allow undo for Fiducial lists (currently no effect)