• FreeviewDevelopment

To implement before the upcoming release of freeview

1. Link the surfaces together (i.e. when you click on a vertex in the inflated surface, it should go to that vertex on the white and pial) & show identical vertex information in the Voxel Info panel

   • we talked about loading a surface set which would have all the pertinent surfaces linked (but would like ability to turn off surfaces that are within the set); having a separate cursor for this; overriding the info in the Voxel Info Panel to display info based on a specific vertex

Bugs

1. When load an overlay with a specified threshold from the commandline, clicking on the 3D surface changes the threshold back to the default - Possibly fixed
2. When you enter in values for Mid point, it doesn't always change the display (hitting enter doesn't seem to do anything)

Keyboard shortcuts to implement

1. Ctrl+f to turn on and off all surfaces currently loaded.
2. Recon edit button
3. ROI edit button
4. Point set edit button

5. Lock & unlock a file

6. Ctrl+y redo an action

High priority

1. when loading ?h.inflated, specify default offsets 45 for rh and -45 for lh

Medium priority

1. List the # of control points currently loaded/placed in one of the panels
2. When you uncheck a layer, do not make it the active volume (highlight it)

Low priority

1. By default, turn off the 3D frames and slices
2. When right click on Volumes, Surfaces, ROI, etc. headings in layer list, can choose 'Hide all' and 'Show all'.
3. Add the ability to use a long cursor in 3D
4. When loading a ?h.curv file, make the default 'threshold' instead of 'binary'
5. When loading a .label file, the browse window should go to the label directory by default if it exists (otherwise, stay in the current directory)

6. When loading an overlay, go to the browse files window by default & have it look for 'All files' as default

7. When choose 'Save As', use current name of layer as name it should be saved as (user still has to hit 'ok' to agree to that name) instead of New Volume (in the cases where it was renamed from New Volume after it was loaded)

8. Right click on Volumes, ROIs, Point set headings gives option to 'Save All'. This should save checked and unchecked volumes and work similar to TrackVis in that it will save with their current name (although it would be better if it could prompt you through each layer and ask if you want to save it with its current name)

9. Ability to resize Layer list window to make it longer
10. Ability to change opacity of the 3D frames so can see anatomy and tract or surface at same time
11. Ability to view only select 3D frames (i.e. just the coronal plane and not the axial or sagittal) - useful for paper figures

Priority to be determined

1. Ability to draw a label on the surface (including all the options tksurfer has, e.g. fill up to curvature, etc.)
2. Ability to clone from another volume
3. Display talairach and MNI305 coords in the Mouse/Cursor information panel

4. Create script to allow freeview to recognize the recon directory structure. For Allison, ideal command line would be:
   

   • freeview bert -v brainmask wm T1 -surfs -aseg -aparc -cp

   • which would load the volumes brainmask.mgz, wm.mgz, T1.mgz; load all the surfaces (?h.white, ?h.pial, ?h.inflated); load the aseg.mgz with the FreeSurferColorLUT chosen; load the ?h.aparc.annot; and load the control.dat file, if any, saved in the tmp dir. In addition, the ability to use -f (surf dir) and -l (label dir) without specifying the full path.
5. When load inflated surface, don't show inflated surface lines in 2D view

6. When load inflated surface, it shouldn't be viewable at the same time as pial & white surfaces in the 3D view

7. When clicking on a point on the 2D surface, automatically move the cursor in the 3D view to the closest point on the surface to that point in the volume
8. Ability to load multiple labels from the command line
9. Consider changing the M button to an All button that allows you to turn off and on all surfaces.

Should be discussed to see if we all agree

1. When load a label, have it viewable in the surface and the volume (and only have to do -l on the command line for this).
2. Allison wishes for a command line option and section on the GUI that allows users to load all the "basic" recon results. They wouldn't have to list out the path or browse for these files because they will always be in the same location: ?h.curv, ?.thickness, ?h.sulc, ?h.aparc.annot, ?h.aparc.a2009s.annot. The M, I, W, P, and O surface buttons could be repurposed for this.
3. In Recon Edit box, should value range a user can't draw on (5-250) be grayed out so they cannot change this? If they really wanted to do it, they can do it from the voxel edit mode.
4. In the surfaces control panel, under Curvature, it should say "Load" instead of "Reload" because reload implies you will use the same file already loaded
5. In the surfaces control panel, perhaps change "Show vertices" to "Highlight vertices" since the vertices are already visible in mesh mode (and this implies users weren't already looking at them)
6. When have the inflated surface loaded and change the opacity, I'm not sure it's doing what a user would want
7. In the surfaces control panel, when click on 'Overlay', the options are 'Load generic' or 'Load correlation'. Not sure what 'generic' is in this case. Is there a better term for this?
8. It is unclear what midpoint and slope do when different files are loaded

Done!

1. When in Recon edit mode, do not allow the drawing of voxels over already existing voxels that fall in the range of 5-250.
2. Assign the ability to change slices to the up and down arrow keys and change the Page Up and Page Down keys to panning
3. Bug: If the aparc.annot is loaded on the ?h.inflated, when you load a .label file, you cannot turn it off