The GUI is not working and showing error messages

[Sushain MagotraParticipant]

Hi there,
After I run the GUI by entering ‘lead’ command in MATLAB ,it opens the GUI but i cannot do anything because if I click anything on the GUI it shows error messages like :

Cell contents reference from a non-cell array object.
Error in lead>handles2options (line 1266)
options.normalize.method=options.normalize.method{get(handles.normmethod,’Value’)};
Error in lead>storeui (line 1144)
options=handles2options(handles);
Error in lead>setdicomin_Callback (line 1028)
storeui(handles);
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in @(hObject,eventdata)lead(‘setdicomin_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback

I am using MATLAB R2013a but don’t know why is it not working.. Any help would be really appreciated.

Thanks
Sushain Magotra

[andreashornKeymaster]

Dear Sushain,

it seems that the problem is simply that SPM is not on your Matlab path.
Lead DBS essentially needs SPM8 or 12 to run. SPM8 is not really supported anymore but should in principle work for most functions. I’d recommend you download SPM12 (http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), save it to a convenient permanent destination and add it to your Matlab path.

I might be wrong with this diagnosis so please write back if this didn’t solve your problem.

Best, Andy

• This reply was modified 3 years, 3 months ago by  andreashorn.

[Sushain MagotraParticipant]

Hello Andy,

Thanks for your help, I installed the SPM 12 and now its working fine. But now I have a new problem :( , when I try to reconstruct the electrode trajectories it shows the following error messages :

Running job #1
————————————————————————
Running ‘Image Calculator’

SPM12: spm_imcalc (v6124) 16:46:30 – 29/03/2016
========================================================================
Failed ‘Image Calculator’
Error using spm_vol>spm_vol_hdr (line 80)
File “Y:\Sushain\lead_dbs\lead_dbs\templates\bb.nii” does not exist.
In file “Y:\Sushain\lead_dbs\lead_dbs\spm12\spm_vol.m” (v5958), function “spm_vol_hdr” at line 80.
In file “Y:\Sushain\lead_dbs\lead_dbs\spm12\spm_vol.m” (v5958), function “spm_vol” at line 61.
In file “Y:\Sushain\lead_dbs\lead_dbs\spm12\spm_imcalc.m” (v6124), function “spm_imcalc” at line 99.
In file “Y:\Sushain\lead_dbs\lead_dbs\spm12\config\spm_cfg_imcalc.m” (v6536), function “my_spm_imcalc” at line 225.

The following modules did not run:
Failed: Image Calculator

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact
#job as displayed in this error message)
——————
Running job #1
——————
Error while evaluating uicontrol Callback

I am not sure whether its the problem with SPM or something else.It says that some file ‘ bb.nii ‘ does not exist.
It would be really great if you could help.
Thanks
Regards
Sushain Magotra

[andreashornKeymaster]

Dear Sushain,

sorry to hear. We did have a small problem with the last release (which is already fixed) but I think it didn’t really concern bb.nii
Just to be sure, I just downloaded the web-version of Lead-DBS myself and found the file bb.nii correctly within the /templates directory. Did you perchance get Lead-DBS completely from github? Because if so, we don’t have all the large datafiles in the git repository. Github is great to get fast bugfixes and updates but you need to once download the whole repository here from the website.

Could you please retry and download Lead-DBS and check yourself whether bb.nii lies within the /templates directory? Then go ahead and replace your old version of it, make sure, it is on the Matlab path and retry?

Please tell us if there are more issues.

Best, Andy

[Sushain MagotraParticipant]

Hello,

I was trying to download Lead-DBS from the website ,but it seems there is some problem with the webpage and when I click download nothing appears but just blank page with the title ‘DOWNLOAD’ at the top.

So, could you please check the webpage and see if the download link is working properly.

Regards
Sushain Magotra

[andreashornKeymaster]

Dear Sushain,

on my end, the download page works fine. We also have continuous downloads from other users.
Maybe you could try using a different browser?
If you still can’t dl the software, please shoot me an email.

Best, Andy

[andreashornKeymaster]

Dear Sushain,

just as a follow up – just realized after sending my last response that the Download page indeed was broken.
Thanks for the hint. I saw you could download now.

Best, Andy

[Sushain MagotraParticipant]

Hey Andy,

Yes, I was finally able to download the lead-DBS from the website and now I have the bb.nii file in the templates directory so its reconstructing the leads and I am even getting the reconstructed file in the output folder of patient.
The reconstruction file consists of coordinates for the lead contacts and even for the trajectories.

But now the problem is that when I check review reconstruction and run lead-DBS ,it does not show the leads and gives the following error:

Error using svd
Input to SVD must not contain NaN or Inf.
Error in null (line 67)
[~,S,V] = svd(A,0);
Error in ea_reconstruction2native (line 24)
orth=null(normtrajvector{side})*(options.elspec.lead_diameter/2);
Error in ea_load_reconstruction (line 20)
ea_reconstruction2native(options);

Error in ea_manualreconstruction (line 38)
[coords_mm,trajectory,markers,elmodel,manually_corrected]=ea_load_reconstruction(options);
Error in ea_autocoord (line 219)
ea_manualreconstruction(mcfig,patientname,options);
Error in lead>run_button_Callback (line 337)
ea_autocoord(options);
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in lead (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in @(hObject,eventdata)lead(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback

Thanks for your quick replies. :)
Regards
Sushain

[andreashornKeymaster]

Hi Sushain,

sorry that you are having so much trouble.. But at least we got one step further.
It could either be a Matlab-version problem or some weird issue with the normalization routine you used.
Could you please tell me which ML version you use, which SPM version you use and which normalization routine you selected/used within Lead-DBS?

Best, Andy

[Sushain MagotraParticipant]

Hi Andy,

I am using MATLAB R2013a and SPM 12 and for normalization i am using SPM12 Segment nonlinear[MR/CT]

Regards
Sushain

[andreashornKeymaster]

Hi,
okay.. this is weird. Could you please write me an email? I couldn’t find yours.
Best, Andy

[Sushain MagotraParticipant]

Hi Andy,

I was trying to visualize the leads and also find VAT .I did all the steps you told i.e running ea_reslice_nii and then doing normalization using ANTs but the normalization does not work properly and shows this error in a pop up window ”antsApplyTransform.exe has stopped working”.

I was only able to visualize the leads in 3D using the non linear segment method but that too was not correct as the leads were horizontally placed instead of being vertical.

The mri images I used were already in .nii format but we only had a sagittal view for postoperative image and no transversal view.Could this be a problem?

I also have mri images in DICOM format but when I converted them into .nii using the toolbox they were also sagittal view so those also did not work as when I reached the reconstruction step it said mask out of bounds.

So, these are the problems I am facing.Your help will be really appreciated.

Regards
Sushain

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