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

Group comparison in Lead Group

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / Group comparison in Lead Group4
Viewing 9 posts - 1 through 9 (of 9 total)
  • Author
    Posts
  • 02/10/2019 at 7:03 PM #6599
    rubenscury
    Participant

    Hi colleagues,
    I’m trying to compare variables between 2 groups in the Lead Group (for example, bad vs good responders on motor outcomes in Parkinson’s disease). Patients were settled in the group I or II. When I run the group comparison (two sample t-test) after prepare stats, it appears a screen with “normalized volume intersections, left hemisphere” for example, and “t-value=NaN, p-value=Nan”….I don’t know what is going wrong….Did anybody succeed with group comparison t-test analysis?

    Many thanks
    Rubens

    02/11/2019 at 9:51 AM #6603
    andreashorn
    Keymaster

    Hi Rubens,

    good to hear from you – could it be that the sample size is too small for a t-test? What is your N of the two groups?
    Once you click the button, the raw data should appear in your Matlab workspace as well, so you can easily export and do stats elsewhere, as well.

    Hope that helps!

    Best, Andy

    03/15/2019 at 10:14 PM #6985
    rubenscury
    Participant

    Thanks Andy,

    I am comparing group 1 (N=20) vs group 2 (N=10)….it still appears the following message in the matlab workspace:
    Volume Intersections, both hemispheres

    h =

    NaN

    p =

    NaN

    ci =

    NaN
    NaN

    and so on….

    The correlation is working very well, but the group comparison I am not sure what is happening…

    Many thanks
    Rubens

    03/16/2019 at 12:46 PM #6988
    andreashorn
    Keymaster

    Hi Rubens,

    maybe your regressor is set up incorrectly. It should be all ones for group 1 and all zeros for group 2.
    So assume you have e.g. 5 top responders and 5 poor responders and want to run a paired t-test on their VTA intersections with the STN, then you would add a vector like
    [1
    1
    1
    1
    1
    0
    0
    0
    0
    0];
    as the regressor. Then click on the group comparison button.

    And then it should work.

    Best, Andy

    03/16/2019 at 12:47 PM #6989
    andreashorn
    Keymaster

    (of note, the word “regressor” is wrong here, it has some historic reasons why I’m used to reference the variables entered into lead group as “regressors”). In this case, it’s basically just a variable that codes for the groups.

    03/16/2019 at 2:29 PM #6990
    rubenscury
    Participant

    Very nice Andy, thanks a lot

    I am also trying to change the “brain parcellation” in the Lead Group. For exemple, move from AICHA to Harvard Oxoford…..
    In the Lead Group, all the patients and the variables are already set. But when I change in the link “which brain parcellation to use:” from AICHA to Harvard Oxoford and run “Prepare Stats”, in the “fiber count to” still appears the AICHA parcellation (G_Frontal_Sup_Orb…etc…)…i.e. it is not changing the brain area….

    Would you have any insight for what is going wrong?

    Again, thanks for your attention
    Best
    Rubens

    03/16/2019 at 2:34 PM #6991
    andreashorn
    Keymaster

    No it should update like that.
    You probably could update to 2.2 and test again?

    Best, Andy

    03/16/2019 at 3:30 PM #6992
    andreashorn
    Keymaster

    Hi Rubens,

    I also just noticed that there was a serious bug in the ttest functionality in the “normalized” VTA reports.
    https://github.com/netstim/leaddbs/commit/54fdc91f0570d442388f6030f58a56c9337ccf0f#diff-c406b0ce9f31d9fc6834ffef4b9e7f78R917
    See this edit – if you need it now would need to change lines 917, 920 and 923 accordingly (or wait for the next update).

    Thanks! Andy

    03/16/2019 at 6:06 PM #6993
    rubenscury
    Participant

    Thanks Andy,

    The “brain parcellation” problem I solved, it is working normally…

    The “t-test” issue I’ll try later and see….

    Best
    Rubens

  • Author
    Posts
Viewing 9 posts - 1 through 9 (of 9 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 @JNeuromod: Editor's Choice #openaccess in the current issue! https://t.co/dzs3jy4Gs0 https://t.co/7ybpSMUevp

    2d
  • Tweet Avatar
    leaddbs
    @leaddbs
    Very cool! 👇👇 https://t.co/1x9pfsiFI2

    3d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @DrPhilipMosley: Modulation of emotional processing with right (ventromedial) subthalamic low-frequency #deepbrainstimulation Recap… https://t.co/zonHML9Ua2

    3d

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