Lead-DBS
  • Home
  • About
    • Quickstart Primer (Post-OP MR-Scans)
    • Data & Code inclusion philosophy
    • Quickstart Primer (Post-OP CT-Scans)
    • Deep Brain Stimulation
    • Lead Connectome
    • Publications
    • List of Lead-DBS dependencies
    • Citing Lead-DBS
  • News
  • Contact
  • Help/Support
    • Manual
    • Knowledge Base
      • Atlases/Resources
        • Subcortical Atlases (MNI-Space)
        • Cortical Atlas Parcellations (MNI-Space)
        • Macaque Atlases (MNI-Space)
        • The DISTAL atlas
        • FEM-based VTA model
        • Normative Connectomes
      • Lead-DBS Methods
        • Subcortical Electrophysiology Mapping (SEM)
        • AC/PC to MNI conversion
        • Connectivity Benefit Mapping
      • Other Videos
      • Screenshots
      • Walkthrough-Videos
    • Slack User Channel
    • Forum
  • Workshops
    • Past workshops
      • Berlin 2016
      • Shanghai September 2018
      • Hamburg February 2019
    • Berlin September 2019
    • Machine Learning – Berlin September 2019
    • Brisbane February 2020
  • Download
  • Lead-Connectome
  • Search
  • Menu Menu

Matlab Toolbxes

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Matlab Toolbxes4
Viewing 8 posts - 1 through 8 (of 8 total)
  • Author
    Posts
  • 03/29/2016 at 10:17 PM #870
    Bechir
    Participant

    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

    03/29/2016 at 10:33 PM #871
    andreashorn
    Keymaster

    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

    03/29/2016 at 10:38 PM #872
    Bechir
    Participant

    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

    03/29/2016 at 11:21 PM #874
    andreashorn
    Keymaster

    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

    03/30/2016 at 8:02 AM #875
    Bechir
    Participant

    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

    03/30/2016 at 3:49 PM #877
    andreashorn
    Keymaster

    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

    05/18/2016 at 6:37 PM #983
    sahbi_m
    Participant

    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

    05/18/2016 at 6:52 PM #984
    sahbi_m
    Participant

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

    best regards,
    sahbi

  • Author
    Posts
Viewing 8 posts - 1 through 8 (of 8 total)
  • The forum ‘Support forum ARCHIVED – Please use Slack Channel instead’ is closed to new topics and replies.

Your Account

Log In
Register

Forum Statistics

Registered Users
132
Forums
1
Topics
185
Replies
607
Topic Tags
81

Subscribe to our newsletter

Latest Tweets

  • Tweet Avatar
    leaddbs
    @leaddbs
    Nice study led by @DrAlfonsoFasano on GPi-DBS for pediatric dystonia. Voxel cluster most associated with clinical i… https://t.co/IScNqVQX94

    22h
  • Tweet Avatar
    leaddbs
    @leaddbs
    This is probably the oldest easteregg in @leaddbs, surprising that it survived until now from the very first releas… https://t.co/qqcUBw3nW1

    5d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @Chencheng_Zhang: Our study demonstrates the beneficial effects of GPi-DBS for treating camptocormia in PD patients in the short term https://t.co/eq03g2oKb2

    5d

Recent Posts

  • Lead-DBS on the cover of NeuroImage
  • Lead-DBS on the cover of Biological Psychiatry
  • Lead-DBS on the cover of Annals of Neurology
  • Crucial methodological updates for Lead-DBS
  • 2nd Lead-DBS Workshop in Shanghai, China

Archives

  • September 2020
  • June 2019
  • November 2018
  • September 2018
  • August 2018
  • March 2018
  • November 2017
  • September 2017
  • July 2017
  • April 2017
  • July 2016
  • June 2016
  • May 2016
  • March 2016
  • December 2015
  • November 2015
  • April 2015
  • January 2015
  • December 2014
  • October 2014
  • September 2014
  • July 2014
  • June 2014

Impressum & Datenschutzerklärung

Scroll to top