error using pre-Reconstruct

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  • 02/08/2018 at 11:26 AM #4123
    Nabkr
    Participant

    Hi Lead-DBS team,
    I am trying to use the Lead-DBS for the first time with preoperative MRI and postoperative CT scan. After following the manual I was able to complete DICOM export, coregistration and Normalisation without any error but while doing the pre-Reconstruct, it gives an error saying:

    Estimated point not yet defined. Using second empirical point.
    Subscript indices must either be real positive integers or logicals.

    Error in ea_reconstruct_trajectory (line 226)
    mask(round(estpoint(2)-options.maskwindow : estpoint(2)+options.maskwindow), …

    Error in ea_reconstruct (line 45)
    [trajectory,trajvector]=ea_reconstruct_trajectory(trajectory,lnii,side,refine,options);

    Error in ea_runtraccore (line 37)
    [coords,trajvector{side},trajectory{side},tramat]=ea_reconstruct(options.patientname,options,side,lnii);

    Error in ea_autocoord (line 199)
    [coords_mm,trajectory,markers]=ea_runtraccore(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

    My settings for pre-Reconstruct was Target: STN,GPi or Vim and mask window size: auto. I could not change the Method part as it is locked in TRAC/CORE (Horn 2015).

    Your help would be really appreciated.

    Many thanks in advance.

    Regards,
    Nabin

    02/08/2018 at 11:31 AM #4124
    andreashorn
    Keymaster

    Hi Nabin,

    maybe first step is to change the entrypoint to “Manual” and click on the leads when asked.
    https://leaddbs.gitbooks.io/leaddbs-manual/content/Reconstruction%20of%20Electrode%20Trajectory.html

    Best, Andy

    02/08/2018 at 2:23 PM #4125
    Nabkr
    Participant

    Thank you Andy. Got through that step. But it is taking taking really long to write out 2D . Is it usual ? Also in the tutorial video it says it takes a while, so was wondering if it is something that needs overnight ? Say in a PC with 8GB RAM, 3 ghz processor running MATLAB2015.

    Thanks again.

    Best,
    Nabin

    02/08/2018 at 2:32 PM #4126
    andreashorn
    Keymaster

    To write out 2D results you mean?
    The step that takes long is the ea_screenshot function which uses myaa (antialiasing) code to write out high resolution figures. Could in theory bypass that and use a simple saveas() command if the slow speed bugs you too much. Guess it also depends on the atlas. Does 3D visualization work and did you check reconstruction in the intermediate step?

    Best, Andy

    02/08/2018 at 3:15 PM #4127
    Nabkr
    Participant

    Thanks Andy. Yes, I checked the recontruction as explained also in the video and the 3D visualization also works fine. also, I figured out that its my Matlab, somehow it gets stuck after some steps. I closed all, restarted the matlab again and did write out to 2D and it works fine now.

    Many thanks again for your prompt support. Really appreciate.

    Best,
    Nabin

    02/08/2018 at 3:50 PM #4128
    andreashorn
    Keymaster

    Great, glad that it works!

    Best, Andy

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