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

Running in patient space only

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Running in patient space only4

Tagged: Native Space

Viewing 7 posts - 1 through 7 (of 7 total)
  • Author
    Posts
  • 12/06/2019 at 4:15 PM #8812
    tsieger
    Participant

    Hi,
    would it be possible to use Lead-DBS to work solely in patient’s native space, please? For example, to reconstruct and extract stimulation electrode from non-normalized MRI, or compute VTA in native space? For now, it seems that reconstruction strictly requires normalized images.

    My use case would be to reconstruct the electrodes in native space (before any non-linear mapping took place) and visualize VTA in native space too, superimposing the VTA on patient’s preop image.

    Well, I understand that normalization would be needed to compute VTA (in order to know the distribution of WM/GM), or to show atlases, available in MNI, in native space (to determine the mapping between native and MNI space). But perhaps this would only pose “side steps”, while the main processing would take place in native space?

    Thanks.
    Best regards,
    Tomas

    12/06/2019 at 4:32 PM #8813
    andreashorn
    Keymaster

    Hi hi, yes, this already works – but you have to run the normalization once.
    Then just visualize in native space instead of MNI and do your VTA calculations there.

    12/06/2019 at 5:57 PM #8819
    tsieger
    Participant

    Thanks. Still, is it possible to extract electrodes in native space, in patient’s MRI being not affected in a nonlinear way?

    12/06/2019 at 6:37 PM #8820
    andreashorn
    Keymaster

    Yes of course that’s a core feature of Lead-DBS. In the first popup under 7. Visualization simply choose native space and then 3D visualize which will be in native space. If you calculate a VTA there, it will be calculated in native space. You still have to run normalization to do so but the results will not be affected by this (only the atlas nuclei will be based on the normalization).

    12/09/2019 at 11:13 AM #8833
    tsieger
    Participant

    OK, VTA can be computed in native space.
    However, it seems that electrode reconstruction can be performed in normalized space only, as when I attempt to pre-reconstruct electrodes without normalizing first, it fails with: glpostop_tra.nii" does not exist., even though I choose the ‘Native Patient Space’ option under ‘7. Visualization’.
    Maybe, I’m missing something.

    12/09/2019 at 11:48 AM #8837
    andreashorn
    Keymaster

    Yes, you always need to run normalizations. However, that doesn’t mean they are actually used.
    For prereconstruction, some of the algorithms need some waypoints that are defined in MNI space and then transformed to native space.
    So again i) yes you will always need to run normalizations in Lead-DBS but ii) you can still use the native space reconstructions that do not really use the normalization and iii) if you use atlases in native space that are not manually reconstructed, the inverse of the normalization will be used.

    Best, Andy

    12/09/2019 at 1:55 PM #8841
    tsieger
    Participant

    Great, thanks a lot.
    Tomas

  • Author
    Posts
Viewing 7 posts - 1 through 7 (of 7 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
131
Forums
1
Topics
185
Replies
607
Topic Tags
81

Subscribe to our newsletter

Latest Tweets

  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @neumann_wj: Our #ECG contamination paper on implantable bidirectional brain stimulation systems is live. Great and fast paced c… https://t.co/Rkwp86ZxKE

    3d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @andreashorn_: Clinically relevant study showing ECG artifacts are higher when IPG implanted on the left side. 👏👏 this will likely… https://t.co/ostng3NZxN

    3d
  • Tweet Avatar
    leaddbs
    @leaddbs
    Interesting single center case series with CM + ANT-DBS vs. CM-DBS only in 16 children and adults with drug-resista… https://t.co/0gzbgQlHud

    4d

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