Visualisation in Native space

[DanLumsden]

Dear All
Thank you for producing such an excellent resource! I’m new to Lead-DBS, running through Matlab R2018B on a MacBook. The pipe line seems to work very smoothly, but I’ve run into difficulties with the visualisation steps. visualisation in template space work very nicely, but when I try to visualise in native space, the following error message comes up:

Error using ea_smoothpatch (line 58)
The vertice list is not a m x 3 array

Error in ea_genatlastable (line 255)
fv=ea_smoothpatch(fv,[],ceil(options.prefs.hullsmooth/2));

Error in ea_showatlas (line 50)
atlases=ea_genatlastable(atlases,ea_space(options,’atlases’),options,mifix);

Error in ea_elvis (line 331)
atlases = ea_showatlas(resultfig,elstruct,options);

Error in ea_write (line 42)
resultfig=ea_elvis(options);

Error in ea_autocoord (line 316)
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.

All the steps prior to visualisation work fine (co-registrations, normalisations etc). I’d be very grateful on any advice on how to fix the error (and apologies in advance if this is something obvious I’m missing!).

[andreashorn]

Hi Daniel, could you try this with a different atlas (e.g. the DISTAL minimal) one first and see if that works?
I think the problem is of an empty nifti file which could happen in complicated atlases with small nuclei. We somehow nearly never work in native space, that’s why not every error is ironed out there.

[DanLumsden]

Andreas

Thank you so much for your quick reply. I’ve tried this PM with a number of the atlases and I get exactly the same error message.

[andreashorn]

Hi Daniel,

thanks for reporting this since it was a real bug (only was able to test/reproduce today). I just fixed it and pushed the fix to github. In ~6 hours time or so, you should be able to run Install > Install Developer Version from the Lead-DBS GUI menu to get the fix installed. Then it should work again.
Could be you’d need to delete the /atlases folder inside your patient folder once but think it should work without that.

Best, Andy

[DanLumsden]

Andy

Thanks again for taking the time to look into this. It seems to be working fine now!

Dan

[andreashorn]

Great, glad to hear! A

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