Electrophysiological Atlas of GPi Activity (Neumann 2017) included in Lead-DBS v2.0.0.6

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Inside a new version of Lead-DBS (v2.0.0.6) released yesterday, we included the pallidal theta activity sweet spot defined in A localized pallidal physiomarker in cervical dystonia as well as optimal stimulation targets defined in Thomas Schönecker‘s Article Postoperative MRI localisation of electrodes and clinical ef… and Philip Starr’s Article Microelectrode-guided implantation of deep brain stimulators….

 Since all three spots fall into a very similar region of the GPi, this atlas gives some summarizing evidence for an optimal target inside the GPi. Of note, the target falls into the sensorimotor part of the GPi as defined in

We further included the CIT168 subcortical atlas defined in A High-Resolution Probabilistic In Vivo Atlas of Human Subco… that Wolfgang Pauli and colleagues from Caltech graciously shared for inclusion in Lead-DBS.

Furthermore, the new Schäfer parcellations defined in Local-Global Parcellation of the Human Cerebral Cortex from … that further subdivide the famous 7/17 rs-fMRI brain parcellation established by B.T. Thomas Yeo et al in The organization of the human cerebral cortex estimated by f…  have been added for DBS connectivity analyses.
Last but not least, we included lrnlab.org‘s (PIs Stephen Coombes & David Villaincourt) HMAT
Three-dimensional locations and boundaries of motor and prem… and S-MATT A Template and Probabilistic Atlas of the Human Sensorimotor…  templates of the sensorimotor cortex and -tract as brain parcellations for connectivity analyses in Lead-DBS and Lead-Connectome (for more information on these very helpful templates see http://lrnlab.org/).
For an updated list of subcortical atlases in Lead-DBS see http://www.lead-dbs.org/?page_id=45, for a list of whole-brain / connectivity brain parcellations see http://www.lead-dbs.org/?page_id=1004.

New SEM study out: “Relating pallidal theta activity to dystonic symptoms and anatomy of the GPi”

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In a new study (A localized pallidal physiomarker in cervical dystonia) led by Wolf-Julian Neumann with Siobhan Ewert, Julius Huebl, Christof Brücke, Gerd-Helge Schneider and Andrea A Kühn, we were able to relate pallidal theta power to dystonic symptom severity for the first time.
Furthermore, using the “Subcortical Electrophysiology Mapping (SEM)” approach developed as part of Lead-DBS (implemented inside the “Lead Group” module), we were able to robustly localize theta activity to an anatomical subpart of the internal pallidum that most likely corresponds to its sensorimotor functional zone (based on an atlas developed by Siobhan Ewert et al. (Toward defining deep brain stimulation targets in MNI space:…).
The same approach had been used before to localize beta power in PD within the subthalamic nucleus (Toward an Electrophysiological ” Sweet Spot ” for Deep Brain…) and additionally high frequency oscillations in intraoperative LFP recordings (Localization of beta and high-frequency oscillations within …).
The approach is described in detail in a blog post (http://www.lead-dbs.org/?p=2301) and the Lead-DBS knowledge base (http://www.lead-dbs.org/?page_id=2403) on our website.
We hope that the technique may be applied to localize other LFP signatures to anatomy in the future – again using co-registered recordings of large patient cohorts.

VTA-model support for segmented Leads

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Till Dembek created a segmented Lead Mesh that allows us to run our FEM-calculations (see Connectivity Predicts deep brain stimulation outcome in Park…; model implemented based on SimBio with great help from Johannes Vorwerk) to create VTAs for these electrodes.

Lead-DBS 2.0 out now

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We are proud to release Lead-DBS 2.0 to the community – an open source tool to localize Deep Brain Stimulation (DBS) electrodes in the human brain.
A detailed description of all major new features is available here [http://www.lead-dbs.org/?p=3174], but in a nutshell they are:
  • DISTAL atlas: A detailed brain atlas of the human subcortex based on histology (graciously provided by M. Mallar Chakravarty and Louis Collins), MRI and structural connectivity. It is available in three different nomenclatures, thus serving as a rosetta stone for thalamic nomenclatures (See Siobhan Ewert‘s

    ; for a summary see here [http://www.lead-dbs.org/?page_id=2911]).

  • FEM-based VTA model (beta): To model the physical effects of DBS in the brain, we teamed up with Johannes Vorwerk (SimBio/FieldTrip toolboxes) and Qianqian Fang (Iso2Mesh toolbox). Further help was provided by Ningfei Li (integration inside Lead-DBS), Robert Oostenveld (Initial counseling and help with FieldTrip-related code). This is the first open-source pipeline to model volumes of tissue activated (VTA) as a one-step solution (see Connectivity Predicts deep brain stimulation outcome in Park…and this page [http://www.lead-dbs.org/?page_id=3291] for details).
  • Human Motor Thalamus Atlas: Graciously provided by Igor & Kristy Ilinsky, the human motor thalamus settles controversies about motor projections in the human thalamus. It is based on specialized histological stains and was precisely co-registered to ICBM 2009b space. For more information about the dataset, see [http://www.humanmotorthalamus.com].
  • PaCER: A fully automated method to precisely reconstruct DBS electrode localizations based on postoperative CT data will soon be published by Andreas Husch (Hertel group, Luxembourg) and was graciously provided to Lead-DBS. For more information about PaCER, see [https://adhusch.github.io/PaCER/].
  • MER-Mapping: Ari Kappel (Richardson lab, Pittsburgh) and Chadwick Boulay (Sachs lab, Ottawa) created an intuitive and precise tool to combine DBS reconstructions with microelectrode recordings within Lead-DBS.
  • Multiple novel atlases: In total, Lead-DBS now comes with 23 subcortical atlases [http://www.lead-dbs.org/?page_id=45] and 14 whole-brain parcellations [http://www.lead-dbs.org/?page_id=1004] suited for connectomics.
  • Enhanced workflows: We re-designed large parts of the registration pipeline. For normalization strategies, all SPM routines, ANTs, FSL’s FNIRT and a MaGET-brain like procedure are available directly in Matlab (and without the need to install anything else).
We hope you like our new release – and please don’t hesitate to spread the word to colleagues in the DBS field. To download Lead-DBS now, see [http://www.lead-dbs.org].

DISTAL Atlas methods summary, data out soon

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Summary of novel subcortical atlas that is “made for Lead-DBS”, based on multispectral high-resolution MNI template, histology and structural connectivity (Ewert et al., 2017) here:
http://www.lead-dbs.org/?page_id=2911
Dataset out soon, original publication here:http://www.sciencedirect.com/science/journal/aip/10538119?sdc=1

Major update of Lead-DBS out (v.1.6.5)

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Summary here http://us8.campaign-archive2.com/?u=a5b93846a3a2a714edbcce8ef&id=7038e497df
– Drag’n’Drop support
– Improved ANTs presets
– New Check Normalization viewer
– New NIfTI image classifier
– New atlases (PPN Alho 2017 atlas Magnetic resonance diffusion tensor imaging for the peduncul…, cerebellar parcellations)