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

General discussion

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / General discussion4

Tagged: OS

Viewing 7 posts - 16 through 22 (of 22 total)
← 1 2
  • Author
    Posts
  • 10/13/2017 at 7:02 PM #3561
    Alexandre
    Participant

    Thank you! very useful

    11/20/2017 at 9:40 PM #3759
    Alexandre
    Participant

    Thank you, it was of great help.

    I was going through the stimulation folders and ea_stats file and I could find the VTAs volume. Is there a way to find the VTAs diameter or radius?

    Regards,

    Alexandre

    07/05/2018 at 11:44 AM #5041
    rubenscury
    Participant

    Dear Andreas,
    I’m trying to coregister the images but it is not working…the error below appears in the matlab,
    I’m using anat_1.ii anat_2.nii postop_ct.nii…..

    I’ve already deleted and reinstalled the lead DBS, but the error continues….
    Can you help me?
    Many thanks

    ANTs LINEAR registration done.
    Coregistration done.
    Tonemapping CT… Done. (2.1754 s)

    Exporting coregistration check images to /Users/rubenscury/Desktop/vanilson sn/checkreg…
    Tonemapping CT… Done. (0.8466 s)
    Images aren’t the same size!
    Done.
    Undefined function or variable ‘cfg_util_persistent’.

    Error in cfg_util (line 433)
    [c0, jobs] = cfg_util_persistent;

    Error in spm_jobman (line 246)
    cjob = cfg_util(‘initjob’, mljob);

    Error in ea_docoreg_spm (line 49)
    spm_jobman(‘run’,{matlabbatch});

    Error in ea_coreg2images (line 37)
    affinefile =
    ea_docoreg_spm(options,appendcommaone(moving),appendcommaone(fixed),’nmi’,1,commaoneotherfiles,writeoutmat,interp);

    Error in ea_coreg_all_mri (line 16)
    ea_coreg2images(options,[directory,presentfiles{coregfi}],[directory,presentfiles{1}],[directory,presentfiles{coregfi}]);

    Error in ea_checkcoregallmri (line 9)
    ea_coreg_all_mri(options,usebrainmask)

    Error in ea_autocoord (line 140)
    ea_checkcoregallmri(options,0,1); % check and coregister all
    preoperative MRIs here.

    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
    @(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))

    Error while evaluating UIControl Callback

    07/16/2018 at 11:40 AM #5097
    loreent
    Participant

    Dear lead-dbs team,

    I have a general question regarding OSs, hope you can help. I have been running lead-dbs without problems on my local OS (macOS Sierra, v.10.12.6). Recently we have been trying to move the computations using lead-dbs connectome to our computing cluster for resting state analysis, but here the pipeline (Coregister with SPM/ANTs, Normalize with ANTs, functional connectivity processes) crashes.

    Based on the error message (see below), I believe this has to do with an incompatibility stemming from the OS of the virtual machine I am using to push jobs onto the cluster, which runs CentOS 7. As far as I can tell, CentOS 7 only supports glibc 2.17. Can you please advise on whether the VM OS could indeed be the source of the problem, and if so, is a CentOS-compatible version available or planned?

    Thank you for your help!
    Best wishes, Loreen

    Here is the error message I received:

    Done preprocessing fMRI data.
    No timecourses found, processing…
    ~/lead/ext_libs/ANTs/antsApplyTransforms.glnxa64: /lib64/libc.so.6: version `GLIBC_2.18′ not found (required by ~/lead/ext_libs/support/libstdc++.so.6)

    Error using copyfile
    cp: der Aufruf von stat für
    “~/001/templates/labeling/wrisk_parcel.nii”
    ist nicht möglich: Datei oder Verzeichnis nicht gefunden

    Error in ea_warp_parcellation (line 65)
    copyfile([directory,’templates’,filesep,’labeling’,filesep,’w’,options.lc.general.parcellation,’.nii’],…

    Error in ea_extract_timecourses (line 6)
    ea_warp_parcellation(options.prefs.pprest,’rest’,options);

    Error in ea_createCM_fmri (line 15)
    gmtc=ea_extract_timecourses(options);

    Error in ea_perform_lc (line 81)
    [fMRI_CM, gmtc]=ea_createCM_fmri(options);

    Error in ea_autocoord (line 179)
    ea_perform_lc(options);

    Error in ea_run (line 96)
    ea_autocoord(options);

    Error in lead_connectome>runsavebutn_Callback (line 317)
    ea_run(‘run’,options);

    Error in gui_mainfcn (line 95)
    feval(varargin{:});

    Error in lead_connectome (line 42)
    gui_mainfcn(gui_State, varargin{:});

    Error in
    matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_connectome(‘runsavebutn_Callback’,hObject,eventdata,guidata(hObject))
    Error while evaluating UIControl Callback

    07/19/2018 at 9:20 PM #5130
    rubenscury
    Participant

    Dear colleagues,

    We’ve been working with DBS targeting the cerebellum (dentate nucleus). Does anyone know if there is any atlas in the Lead-DBS that see the cerebellum? If the answer is not, can I import an atlas into the Lead-DBS?

    Best
    Rubens

    09/11/2018 at 6:57 PM #5417
    rubenscury
    Participant

    Dear colleagues,

    In order to walk through all lead-dbs tools, what package in Matlab should I download? 1) computational finance, 2) control system, 3) image processing and computer vision, 4) signal processing, 5) computational biology and 6) data analytics?

    I did not find this information in the manual,

    Regards
    Rubens

    09/11/2018 at 7:36 PM #5418
    andreashorn
    Keymaster

    Hi rubenscury,

    re the cerebellum – see the labeling folder which has the suit atlas and the yeo cerebellar functional zones atlas.
    You can try to use ea_labeling2atlas(‘Cerebellum_SUIT (Diedrichsen 2006)’) to convert the labeling into an atlas – but I’m not 100% sure if it will work. If not need to do manually (just put nifti files in the folders, ignore the atlas_index.mat and gm.nii files that will be built automatically.

    Re toolboxes I think you need stats & machinelearning as well as image processing optimally. Most things should work without but some functions need them.

    Best, Andy

  • Author
    Posts
Viewing 7 posts - 16 through 22 (of 22 total)
← 1 2
  • The topic ‘General discussion’ is closed to new 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 @nastasiayendiki: 1/ Update from round 2 of the IronTract Challenge (for more, watch out for #ISMRM2021 talk by @chiaramff - with… https://t.co/Fgxg8kds4d

    2d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @andreashorn_: I was very honored about the possibility to interview one of my true heroes in the field of DBS modeling in a new… https://t.co/GTtgDOwZBi

    4d
  • Tweet Avatar
    leaddbs
    @leaddbs
    RT @MGHNeuroSci: Mark Richardson, MD, PhD, director of Functional Neurosurgery at @mghneurosurg, discusses the successful use of dee… https://t.co/zyPXo98pvt

    4d

Recent Posts

  • Lead-DBS v2.5 out now!
  • 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

Archives

  • March 2021
  • 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