Matlab Toolbxes

[Bechir]

Hello
When I tried to use Lead-DBS I realized that Matlab requires the “Statistics and Machine Learning” toolbox from Mathworks, so I bought it. But it still does not finish reconstruction.
Error message says that it requires another toolbox of Matlab: “Signal Processing Toolbox”.
I think it’s helpful to specify all the optional toolboxes one should buy from Mathworks in order to make Lead-DBS work.
All the best
Bechir

[andreashorn]

Dear Bechir,

thanks for your feedback and sorry to hear that you went through that trouble. We’ll add these toolboxes to the requirements sections.
The toolboxes I use to develop Lead-DBS are the following one:

• Image Processing Toolbox
• Signal Processing Toolbox
• Curve Fitting Toolbox
• Statistics and Machine Learning Toolbox

However, we always try to make things work with the least number of toolboxes possible. So maybe we could even fix the issue without you needing to buy another toolbox. If you could kindly post the error concerning the Signal Processing Toolbox, maybe I could find alternative functions and post an update that works w/o this toolbox, soon?

Best, Andy

[Bechir]

Thank you very much Andy for prompt answer.
Here is the error message
Best Regards
Bechir

Preparing contrasted volume…
Obj number 1, distance: 79.3737.
Using object 1.
Obj number 3, distance: 93.1312.
Obj number 4, distance: 73.6688.
Using object 4.
Estimated point not yet defined. Using second empirical point.
Lower than z=-15.5 mm. Stopping.
Calculating cross-correlation series for all x and y values within the cuboid volume.
xcorr is not included in your installed products. These products offer
‘xcorr’:
Signal Processing Toolbox

Error in ea_reconstruct_coords (line 41)
[corrs(cnt,:),lags]=xcorr(squeeze(cimat(xx,yy,:)),squeeze(temp(xx,yy,:)));

Error in ea_reconstruct (line 123)
[coords,goodz]=ea_reconstruct_coords(trajectory,trajvector,options);

Error in ea_autocoord (line 129)
[coords,trajvector{side},trajectory{side},tramat]=ea_reconstruct(patientname,options,side);

Error in lead>run_button_Callback (line 333)
ea_autocoord(options);

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

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

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[andreashorn]

Dear Bechir,

I could replace the xcorr function with a custom built one. I’ll upload an update this evening and you should be able to grab it via the green Update button from within Lead in Matlab tomorrow morning at the latest.
Please let me know if there are other functions that are Signal Processing Toolbox dependent (it’s not easy to find out or at least I don’t know how to do this).

Will be happy to make the version run w/o Sig Proc. Tbx.

Best, Andy

[Bechir]

Dear Andy
Thank you for your incredible reactivity !
Now it went further without requiring another tool box function.
Unfortunately I got the following error message.
Thank you for your advice.
Best
Bechir

Preparing contrasted volume…
Obj number 1, distance: 80.242.
Using object 1.
Obj number 2, distance: 92.7863.
Obj number 3, distance: 81.0634.
Obj number 4, distance: 74.2726.
Using object 4.
Estimated point not yet defined. Using second empirical point.
Midpoint is nan. Stopping.
Calculating cross-correlation series for all x and y values within the cuboid volume.
Maximal value was: 1820302.253.
Preparing contrasted volume…
Obj number 2, distance: 80.5069.
Using object 2.
Estimated point not yet defined. Using second empirical point.
Midpoint is nan. Stopping.
Index exceeds matrix dimensions.

Error in ea_sample_cuboid (line 92)
if trajvector(3)<0

Error in ea_reconstruct_coords (line 3)
[cimat,reldist]=ea_sample_cuboid(trajectory,options);

Error in ea_reconstruct (line 123)
[coords,goodz]=ea_reconstruct_coords(trajectory,trajvector,options);

Error in ea_autocoord (line 129)
[coords,trajvector{side},trajectory{side},tramat]=ea_reconstruct(patientname,options,side);

Error in lead>run_button_Callback (line 337)
ea_autocoord(options);

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

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

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[andreashorn]

Hi Bechir,

now it seems that there’s some problem that the algorithm can’t find the trajectory.

What you could do is:
1. Set the Entrypoint to manual. You’ll be prompted to click on the electrodes. Do you see them at all? Has the data been properly normalized?
2. Instead of “auto” in mask size, you can try to enter a number between ~ 7 and 15. This keeps the mask size fixed and helps in some cases.

What dataset are you using? Is it T1-weighted data? Because here, the algorithm sometimes gets lost in the ventricles. If you have a different dataset, maybe try to skip this patient first. I totally need to upload an easy sample dataset one day.

I hope this helps.

Best, Andy

[sahbi_m]

Hi Andy,

Thank you for your reactivity. Actually there was a pretty good progress in my work but unfortunatly usually after the manual correction it shows me up an error message. If you could kindly find below this message which was generated after each saving results (with the espace bar) of a manuel correction.

All my best
sahbi

Reference to non-existent field ‘rawpreniis’.

Error in ea_assignpretra (line 6)
for prenii=1:length(options.prefs.rawpreniis)

Error in ea_native2acpc (line 47)
options=ea_assignpretra(options);

Error in ea_reconstruction2acpc (line 12)
fid=ea_native2acpc(cfg,{directory});

Error in ea_save_reconstruction (line 24)
ea_reconstruction2acpc(options);

Error in ea_manualreconstruction>ea_endfcn (line 120)
ea_save_reconstruction(coords_mm,trajectory,markers,elmodel,1,options);

Error in ea_manualreconstruction>ea_keystr (line 167)
ea_endfcn(mcfig);

Error while evaluating Figure KeyPressFcn

[sahbi_m]

I’m sorry for this message it wasn’t in the right place.
it will be posted in the other conversation.

best regards,
sahbi

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