Localize DBS electrodes

[ada.sevillamu]

Hi,
I was able to run each process of lead dbs some weeks ago. Now, I updated the program and I have some errors, so I am not able to localize dbs electrodes.
First, when I am using Post-Operative CT scans, I run “Check Normalization” and I get these errors:

Preparing images to show Normalization…
No glgrid.nii file found!
Done.
** Process done.
>>

Despite these lines, I continue the steps and when I try to localize the electrodes, I get these errors:

Reference to non-existent field ‘acpc’.

Error in ea_load_reconstruction (line 39)
coords_acpc=reco.acpc.coords_mm;

Error in ea_manualreconstruction (line 38)
[coords_mm,trajectory,markers,elmodel,manually_corrected]=ea_load_reconstruction(options);

Error in ea_autocoord (line 203)
ea_manualreconstruction(mcfig,patientname,options);

Error in ea_run (line 95)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 240)
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

>>

Thank you, Ada

[andreashorn]

Hi Ada,

sorry for the problems,

the “acpc” bug is already known and will be fixed in the next release. In the meantime, please comment (add a ‘%’ in front) line 39 in the ea_load_reconstruction.m file to make it work.

Re. your first error, these are no errors and you should be fine. However, in case nothing happens, please make sure you find a file called “mni_wires.mat” inside lead/templates folder.
If you don’t, you can download the file here (https://dl.dropboxusercontent.com/u/18255196/mni_wires.mat) – or redownload lead-dbs from the website.

Best, Andy

[ada.sevillamu]

Thank you Andy. I solved this problem with your tip, but now, I get some different errors. When I try tolocalize electrodes, I get:

Index exceeds matrix dimensions.

Error in ea_manualreconstruction>updatescene (line 429)
memp_eldist=mean([emp_eldist{1},emp_eldist{2}]);

Error in ea_manualreconstruction (line 43)
updatescene([],[],mcfig);

Error in ea_autocoord (line 203)
ea_manualreconstruction(mcfig,patientname,options);

Error in ea_run (line 95)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 240)
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

>>

Thank you, Ada

[andreashorn]

Hi Ada,

glad it worked.
What you could do is i) try with a “manual” entrypoint, i.e. set the popup menu to “manual” before running the pre-localization step. You’ll be prompted with a window in which you may click on the electrodes within a red rectangle.
If you don’t see the electrodes at all, something went wrong in normalization.
ii) try with another patient – just to verify it works in general on your side. If that works, we can definitely fix it for the current patient, as well.

Best, Andy

[Atefeh]

Hello,
I was aslo able to work with lead DBS 2 weeks ago but now I updated it and it does not work!
when I type lead dbs in the command window, I get these errors:

Error using ea_firstrun
Too many input arguments.

Error in lead_dbs>lead_dbs_OpeningFcn (line 158)
ea_firstrun(handles,options);

Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

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

Error in lead>lead_OpeningFcn (line 79)
lead_dbs;

Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});

I would be grateful, if you could help.

Best wishes,
Atefeh

• This reply was modified 7 years, 10 months ago by Atefeh.

[andreashorn]

Please replace this file: https://dl.dropboxusercontent.com/u/18255196/ea_firstrun.m

[Atefeh]

Thank you so much! It is working now :)

[andreashorn]

Sure, no problem!

[Atefeh]

Hello,
I am trying to normalize the images, but I get this error:

Undefined function or variable “to”.

Error in ea_normalize_ants (line 80)
ea_ants_nonlinear(to,from,[directory,options.prefs.gprenii],weights,metrics,options);

Error in ea_autocoord (line 92)
eval([options.normalize.method,'(options)’]); % triggers the normalization function and passes the options struct to it.

Error in ea_run (line 89)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 192)
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 @(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

I would be happy, if someone could help.

Best,
Atefeh

[andreashorn]

Hi Atefeh,

it seems that some files are not properly installed in your installation. Please try a fresh installation from the website which should fix this.

Best, Andy

[Atefeh]

Hi Andy,

I also installed lead dbs again, but it is still not working…

Best,
Atefeh

[andreashorn]

Okay. Then it seems that the files in your subject directory are not named correctly. Can you tell me which files you put into the patient’s folder?

Also, has it worked for you in the past?

Best, Andy

[Atefeh]

I dont think that it is because of the patient’s folder, because I could localize the electrodes successfully some weeks ago and it is not working anymore now!

Best,
Atefeh

[andreashorn]

Can’t really help you without that information though.. Need some more info to reproduce this and debug.

Does this only happen for this specific patient or for all patients you tried?

[Atefeh]

Here you can see a screen shot of my patient’s folder:
http://tinypic.com/r/2q1xixf/9

It is not working for any patients…

[Author]

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