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

Visualisation in Native space

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Visualisation in Native space4
Viewing 6 posts - 1 through 6 (of 6 total)
  • Author
    Posts
  • 01/03/2019 at 8:09 PM #6260
    DanLumsden
    Participant

    Dear All
    Thank you for producing such an excellent resource! I’m new to Lead-DBS, running through Matlab R2018B on a MacBook. The pipe line seems to work very smoothly, but I’ve run into difficulties with the visualisation steps. visualisation in template space work very nicely, but when I try to visualise in native space, the following error message comes up:

    Error using ea_smoothpatch (line 58)
    The vertice list is not a m x 3 array

    Error in ea_genatlastable (line 255)
    fv=ea_smoothpatch(fv,[],ceil(options.prefs.hullsmooth/2));

    Error in ea_showatlas (line 50)
    atlases=ea_genatlastable(atlases,ea_space(options,’atlases’),options,mifix);

    Error in ea_elvis (line 331)
    atlases = ea_showatlas(resultfig,elstruct,options);

    Error in ea_write (line 42)
    resultfig=ea_elvis(options);

    Error in ea_autocoord (line 316)
    ea_write(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.

    All the steps prior to visualisation work fine (co-registrations, normalisations etc). I’d be very grateful on any advice on how to fix the error (and apologies in advance if this is something obvious I’m missing!).

    01/04/2019 at 1:06 PM #6264
    andreashorn
    Keymaster

    Hi Daniel, could you try this with a different atlas (e.g. the DISTAL minimal) one first and see if that works?
    I think the problem is of an empty nifti file which could happen in complicated atlases with small nuclei. We somehow nearly never work in native space, that’s why not every error is ironed out there.

    01/04/2019 at 10:21 PM #6267
    DanLumsden
    Participant

    Andreas

    Thank you so much for your quick reply. I’ve tried this PM with a number of the atlases and I get exactly the same error message.

    01/05/2019 at 12:45 AM #6270
    andreashorn
    Keymaster

    Hi Daniel,

    thanks for reporting this since it was a real bug (only was able to test/reproduce today). I just fixed it and pushed the fix to github. In ~6 hours time or so, you should be able to run Install > Install Developer Version from the Lead-DBS GUI menu to get the fix installed. Then it should work again.
    Could be you’d need to delete the /atlases folder inside your patient folder once but think it should work without that.

    Best, Andy

    01/06/2019 at 6:19 PM #6282
    DanLumsden
    Participant

    Andy

    Thanks again for taking the time to look into this. It seems to be working fine now!

    Dan

    01/06/2019 at 6:22 PM #6283
    andreashorn
    Keymaster

    Great, glad to hear! A

  • Author
    Posts
Viewing 6 posts - 1 through 6 (of 6 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

    20h
  • 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