Write out 2D error and more

[Nabkr]

Hi Lead DBS team,

I have couple of questions which just came along while using the Lead DBS.
1. There is always this error coming up when I want to write out 2D for only ‘Electrophysiological atlas of GPi activity (Neumann 2017)’ . For other atlases it runs fine.

Exporting 2D slice output…
Electrode(s) k0, tra view: z = -0.82713 mm.
Output argument “sides” (and maybe others) not assigned during call to “ea_add_overlay>detsides”.

Error in ea_add_overlay (line 48)
for side=detsides(atlases.types(atlas))

Error in ea_writeplanes (line 191)
cuts = ea_add_overlay(boundboxmm, cuts, tracor, options);

Error in ea_write (line 35)
cuts=ea_writeplanes(options);

Error in ea_autocoord (line 303)
ea_write(options)

Error in ea_run (line 96)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 187)
ea_run(‘run’,options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead_dbs (line 43)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback.

2. Is there a way to write out several atlases rather than only one automatically at once in 2D ?

3. If I understood correctly, the 2D view is flipped Left-right , Is the 3D view also flipped ?

Many thanks in advance.

best Regards,
Nabin

[andreashorn]

Hi Nabin,

it could well be that the functionality in this (point 1) is currently broken – we’ll investigate and hopefully push fixes to github soon.
Re 2. – not really but you can easily create your own atlases (i.e. combine two) by just creating a new folder with the according nifti files inside (don’t mind the ea_atlas_index.mat and the gm_mask nifti file, these will be generated upon first visualization of the atlas).
3. 2D view is neurological convention (meaning left is left and right is right). Instead, some other programs follow radiological convention (where right is left and left is right, “view from below”). 3D view is not flipped (in 3D it’s all more clear and obvious).

Best, Andy

[Nabkr]

Many thanks Andy.

Regards,
Nabin

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