[Sushain Magotra]

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

[Sushain Magotra]

Hi Andy,

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

Regards
Sushain

[Sushain Magotra]

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

[Sushain Magotra]

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

[Sushain Magotra]

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

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