LEAD-DBS is a MATLAB-toolbox facilitating deep brain stimulation electrode locations and connectomic imaging.
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Latest commit 2c0d836 Feb 20, 2017 @akapp akapp tag color buttons and update ea_keepatlaslabels
also makes all windows black
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Lead_manual Corrected mesoFT stuff. Oct 26, 2015
cfg Drop saving lead scene as matlab figure. Feb 1, 2017
cluster Increased memory for short runs on HMS orchestra Nov 15, 2016
connectomics Ignore infinite values in fMRI seeds Feb 18, 2017
dbshub Fixes for last commit. Oct 4, 2016
dev Revert changes of the electrode template location in the code. Jan 20, 2017
ext_libs switch from mm to slice index in slices feature Feb 20, 2017
helpers (hopefully final) fix of new slices feature. Feb 19, 2017
icons Delete mer.png Feb 15, 2017
legacy Remove unused prefs: prefs.normalize.coreg Feb 2, 2017
ls Commit after cortona. Nov 6, 2014
predict Let manual be available in macaque mode. Feb 15, 2017
support_scripts Further fixes regarding the new template folder structure. Jan 18, 2017
templates rm mrTools for now Feb 13, 2017
toolbox Removed norm functions from toolbox/macaque Jan 16, 2017
tools Further fixes regarding the new template folder structure. Jan 18, 2017
vatmodel Show normalization now also showing (tonemapped) postop_ct Feb 19, 2017
.gitignore Fix compat and add default_prefs Jan 16, 2017
.version.txt v1.6.1.2 Feb 12, 2017
LICENSE.md Updated license to include neuromorphometrics atlas Dec 26, 2016
README.md Updated instructions for installation from Github into Readme.md Jul 19, 2016
ea_absor.m Replaced linsolve with a non-shearing version. Aug 19, 2016
ea_activecontacts.m Last fixes before new minor release. Mar 7, 2016
ea_add_overlay.m Fix 2D output Feb 14, 2017
ea_add_overlay_singlefile.m Fixed paths to atlases in main directory Jan 16, 2017
ea_addnormmethods.m Changed logic of how to determine if norm function is compatible or not. Dec 30, 2016
ea_addobj.m Fixed warpVTA function (now need to homogenize extract_tc_VAT and ext… Dec 6, 2016
ea_addrecentpatient.m Added standalone-mode for lead_connectome Jul 23, 2016
ea_addtsmask.m Show normalization now also showing (tonemapped) postop_ct Feb 19, 2017
ea_amendtoolboxoptions.m Fix to run connectome part from within lead dbs Feb 17, 2017
ea_anatomycontrol.fig switch from mm to slice index in slices feature Feb 20, 2017
ea_anatomycontrol.m switch from mm to slice index in slices feature Feb 20, 2017
ea_anatomyslices.m switch from mm to slice index in slices feature Feb 20, 2017
ea_anatpreprocess.m Skip rocrop but run biasfield correction, images should be Feb 6, 2017
ea_apply_normalization.m Added SUIT based DARTEL normalization Dec 29, 2016
ea_apply_normalization_tofile.m Now atlases and labeling files may be imported from other spaces via … Jan 22, 2017
ea_applynormtofile_menu.m Fixed normtofile for SPM (did only support inverse case so far) Jan 15, 2017
ea_assignbackdrop.m Fixed backdrop selections for other spaces Jan 22, 2017
ea_assignpretra.m Readded compatibility with folders that only contain ea_reconstructio… Dec 14, 2016
ea_autocoord.m Remove unused prefs: prefs.normalize.coreg Feb 2, 2017
ea_build_DTD.m Changed Diffusion Tensor to HARDI (elsewise misleading). Mar 17, 2016
ea_busyaction.m Amend Oct 28, 2016
ea_calc_distance.m Added Manual, next try Jun 24, 2014
ea_centralcomponent.m Replaced imaging toolbox functions (edit 1) Aug 5, 2014
ea_centrality_significance.m Made a release to v1.4.2 Nov 5, 2015
ea_centroid.m Replaced imaging toolbox functions (edit 1) Aug 5, 2014
ea_checkctmrpresent.m Fix auto CT/MR popup selection Feb 15, 2017
ea_checkfiles.m Slices now report mm back Feb 7, 2017
ea_checkforwardinv.m Separate ea_detvoxsize function Jul 27, 2016
ea_checkinstall.m rm macaque from install menu (since now is space) Jan 19, 2017
ea_checkmacaque.m Added normalization to file to Tools menu Jan 15, 2017
ea_checkspm.m Warn user if SPM12 not installed. Dec 12, 2016
ea_checktrajectsanity.m Added Manual, next try Jun 24, 2014
ea_compat_data.m Need to set path before calling getspace Jan 22, 2017
ea_concatfv.m Added cork option in concat_fv Jan 7, 2017
ea_concavehull.m Added Manual, next try Jun 24, 2014
ea_conncomp.m Changed ea_conncomp slightly. Aug 5, 2014
ea_coreg2images.m Fix for hybrid coregs with SPM Feb 17, 2017
ea_coreg_all_mri.m Conform voxel space after coregmrall Feb 19, 2017
ea_coreg_fa.m fix for FA support in multi anatomical setting. Dec 9, 2016
ea_coregctmri_ants.m Added + Subcortical Refine option to ANTs and SPM affine coregistrations Dec 31, 2016
ea_coregctmri_ants_multiple.m Added + Subcortical Refine option to ANTs and SPM affine coregistrations Dec 31, 2016
ea_coregctmri_ants_multiple_refine.m Added + Subcortical Refine option to ANTs and SPM affine coregistrations Dec 31, 2016
ea_coregctmri_ants_refine.m Added + Subcortical Refine option to ANTs and SPM affine coregistrations Dec 31, 2016
ea_coregctmri_brainsfit.m Show image file name during rocrop Nov 29, 2016
ea_coregctmri_brainsfit_multiple.m Show image file name during rocrop Nov 29, 2016
ea_coregmr.m Remove unused prefs: prefs.normalize.coreg Feb 2, 2017
ea_coregmr_ants.m commit ea_coregmr writeout options Jan 26, 2017
ea_coregmr_brainsfit.m commit ea_coregmr writeout options Jan 26, 2017
ea_coregmr_flirt.m commit ea_coregmr writeout options Jan 26, 2017
ea_coregmr_spm.m Add 'writeoutcoreg' option for ea_coregmr_spm. Feb 2, 2017
ea_correctcoords.m Further development of the Hybrid mapping algorithm. Feb 4, 2016
ea_corrplot.m Moved installable items to menu. Sep 5, 2016
ea_corrplot_gen.m Moved pca_templates to helpers/space, show variance explained Feb 10, 2017
ea_create_tpm_darteltemplate.m Making sure TPMs always sum up to 1 for each voxel Feb 17, 2017
ea_credits.m Added many bugfixes, as well as DTI tracking functionally (using DTI&… Feb 7, 2015
ea_crop_nii_bb.m Made a release to v1.4.2 Nov 5, 2015
ea_cylinder.m Merge pull request #67 from QRabbani/master Jul 13, 2016
ea_defaultoptions.m Merge pull request #67 from QRabbani/master Jul 13, 2016
ea_detect_edges_3d.m Ending with ea_dispercent 1 Aug 15, 2016
ea_detstimname.m User is prompted to enter a stimulation label each time. May 30, 2016
ea_detthresh.m Fix for rare occasion of left or right-only mixed atlases. Jul 25, 2016
ea_dicom_import.m Fixed dicom import for non-DICOM-containing folders and multiple sele… Dec 29, 2016
ea_dispbn.m Add incremental update Nov 2, 2015
ea_dispercent.m Fully incorporate FSL FLIRT and FNIRT Nov 14, 2016
ea_docoreg_spm.m Added + Subcortical Refine option to ANTs and SPM affine coregistrations Dec 31, 2016
ea_draggable.m Added Manual, next try Jun 24, 2014
ea_edit_regressor.fig Added support for regressors with 1 value for each hemisphere in lead… Dec 20, 2015
ea_edit_regressor.m Added support for regressors with 1 value for each hemisphere in lead… Dec 20, 2015
ea_elvis.m tag color buttons and update ea_keepatlaslabels Feb 20, 2017
ea_export.m Fix in ea_export for multiple patients Feb 14, 2017
ea_export_ls_index.m Commit after cortona. Nov 6, 2014
ea_export_server.m Merge pull request #67 from QRabbani/master Jul 13, 2016
ea_export_templates.m Revert changes of the electrode template location in the code. Jan 20, 2017
ea_exportisovolume.m Fix in ea_export for multiple patients Feb 14, 2017
ea_exportvatmapping.m Further fix of filepaths Jan 16, 2017
ea_extrapol_coords.m Added Manual, next try Jun 24, 2014
ea_findcoords.m Added Manual, next try Jun 24, 2014
ea_findonemidpoint.m Added initial LEAD-Connectome Apr 18, 2015
ea_firstrun.m Boost startup speed of all lead apps Feb 8, 2017
ea_firstrun_public.m Amend Aug 29, 2016
ea_fit_line.m Major comit for lead connectome introduction. Comit before systematic… May 5, 2015
ea_genatlastable.m Final tweaks for asset import feature. Jan 22, 2017
ea_gencheckreg.m Can now generate checkregfiles from Menu, too Dec 27, 2016
ea_gencontrastimage.m Add ea_delete helper function Nov 2, 2016
ea_gencoregcheckfigs.m Fixed appearances of mni_hires in main folder Jan 16, 2017
ea_genhdtrajectory.m Added Manual, next try Jun 24, 2014
ea_gentargetreport.m Finalized new stimparams settings figure support in lead_group. Feb 22, 2016
ea_genvat_kuncel.m Fix in old vat models as reported by pd/ak Jan 10, 2017
ea_genvat_maedler.m Fix in old vat models as reported by pd/ak Jan 10, 2017
ea_genvat_simbio.m Fix in old (depreciated) vatmodel Jan 29, 2017
ea_genvat_simbio_iso2mesh.m Show normalization now also showing (tonemapped) postop_ct Feb 19, 2017
ea_get_icn.m Added Manual, next try Jun 24, 2014
ea_getearoot.m More deployment support. Aug 29, 2016
ea_getmagetpeers.m Show deformation grid as per TH's idea if prefs is set accordingly. Oct 19, 2016
ea_getnativemni.m ea_getnativemni.m defaults to min space Jan 30, 2017
ea_getpatients.m Foundations of predict module. Feb 14, 2017
ea_getvsn.m Merge pull request #67 from QRabbani/master Jul 13, 2016
ea_handles2lc.m Changed structure in saving lc_opts which now also support storing Dec 26, 2016
ea_handles2options.m Now can add surface seeds for connectome mapper, too. Jan 21, 2017
ea_hotfix.m Update hotfix and patch function Dec 12, 2016
ea_hyperlink_label.m Add hyperlink label Jun 20, 2016
ea_imageclassifier.fig Further fix dcm2niix path handling issue Nov 27, 2016
ea_imageclassifier.m Further fix dcm2niix path handling issue Nov 27, 2016
ea_importcorticalels.m templates/space/ Jan 16, 2017
ea_importfs.m update importfs Jan 16, 2017
ea_imshowpair.m Fix error in hybrid view of 'Check Coregistration' when left clicking Jan 9, 2017
ea_init_coregmrpopup.m Added + Subcortical Refine option to ANTs and SPM affine coregistrations Dec 31, 2016
ea_initrecentpatients.m Added standalone-mode for lead_connectome Jul 23, 2016
ea_isosignificance.m Started to add statistics to isovolumes and to enter DTI info to simb… Sep 28, 2015
ea_keepatlaslabels.m tag color buttons and update ea_keepatlaslabels Feb 20, 2017
ea_largestcomponent.m Update release. Dec 6, 2014
ea_largestcomponent_nii.m Lead group only loads fibers file once in calc_stats now. Mar 14, 2016
ea_leoo_significance.m export R,p for bootstrapping options Dec 21, 2016
ea_leoo_significance_weightedave.m Two new significance measures for point clouds. Dec 21, 2016
ea_leoo_significance_weighteddist.m Two new significance measures for point clouds. Dec 21, 2016
ea_linsolve.m Replaced linsolve with a non-shearing version. Aug 19, 2016
ea_listatlassets.m Foundations of predict module. Feb 14, 2017
ea_load_reconstruction.m Formatting code. Jan 18, 2017
ea_magetcheck_norm_peers.m anat.nii -> anat_t2.nii, novel handling for dominant anatomical images. Dec 9, 2016
ea_manualreconstruction.m fix for unilateral implant Feb 14, 2017
ea_map_coords.m Small fix of fiber normalization Nov 29, 2016
ea_maximize.m Fully incorporate FSL FLIRT and FNIRT Nov 14, 2016
ea_menu_addtransfer.m Added transfer menu to open loaded patients in other leadsuite apps. Nov 6, 2016
ea_mirrorsides.m Fix in viz for lead_group Jan 22, 2017
ea_mod_tex.m Finished PDF-Export from Lead-DBS including 3D PDF Jul 10, 2016
ea_nanmean.m Added isovolume visualization support for 2D-Group visualization. Jul 15, 2015
ea_nc_segment.m Add ea_delete helper function Nov 2, 2016
ea_newseg_pt.m anat.nii -> anat_t2.nii, novel handling for dominant anatomical images. Dec 9, 2016
ea_nice_colors.m Added .mat and .nii files from electrode_models into lead git. Nov 3, 2015
ea_norm_ptspecific_atl.m Further fixes regarding the new template folder structure. Jan 18, 2017
ea_normal.m Update release. Dec 6, 2014
ea_normalize_ants.m ANTs multimodal normalization replaces ANTs unimodal as default, now … Jan 19, 2017
ea_normalize_apply_normalization.m Changed logic of how to determine if norm function is compatible or not. Dec 30, 2016
ea_normalize_fsl.m Fixed appearances of mni_hires in main folder Jan 16, 2017
ea_normalize_maget.m Fixed appearances of mni_hires in main folder Jan 16, 2017
ea_normalize_maget_segment.m Further fixes regarding the new template folder structure. Jan 18, 2017
ea_normalize_maget_segment_se.m Update to new file structure Jan 19, 2017
ea_normalize_reslicepretra.m Changed logic of how to determine if norm function is compatible or not. Dec 30, 2016
ea_normalize_spmdartel.m Fixed shoot & dartel Jan 16, 2017
ea_normalize_spmnewseg.m Changed logic of how to determine if norm function is compatible or not. Dec 30, 2016
ea_normalize_spmshoot.m Support for "packed" spaces Jan 17, 2017
ea_normalize_suit.m Update template file entries for the new templates folder structure. Jan 18, 2017
ea_normsettings_maget.fig Tweak MAGeT setting UI Aug 19, 2016
ea_normsettings_maget.m Tweak MAGeT setting UI Aug 19, 2016
ea_normsettings_maget_segment.fig Tweak MAGeT setting UI Aug 19, 2016
ea_normsettings_maget_segment.m Tweak MAGeT setting UI Aug 19, 2016
ea_openin.m Finished cross-loading to include lead group. Nov 6, 2016
ea_options2handles.m Added .ply and .stl export functions. Moved PDF export from checkbox … Jul 13, 2016
ea_options2tdhandles.m Use listatlassets in lead_anatomy, too Jan 16, 2017
ea_prefs.m Boost startup speed of all lead apps Feb 8, 2017
ea_prefs_default.m Boost startup speed of all lead apps Feb 8, 2017
ea_prefs_default.mat Also included lc options into machine-readeable options Jan 16, 2017
ea_prepare_slice.m Error prompt when mask is out of slice during electrode reconstruction. Dec 1, 2016
ea_ptspecific_atl.m Fix for SE to not interp on atlas warps Feb 6, 2017
ea_rangesearch.m Added Manual, next try Jun 24, 2014
ea_rcpatientscallback.m Added GUI called Lead Anatomy (not yet fully functional) Aug 1, 2016
ea_read_fiducials.m Added Manual, next try Jun 24, 2014
ea_reconstruct.m Added support for novel bounding box. Mar 16, 2016
ea_reconstruct_coords.m Revert changes of the electrode template location in the code. Jan 20, 2017
ea_reconstruct_trajectory.m Resolved left right issue Feb 17, 2017
ea_reconstruction2acpc.m Also store AC & PC coordinates. Dec 12, 2016
ea_reconstruction2mni.m Small fixes for lead-group and assoc. scripts Feb 19, 2017
ea_reconstruction2native.m Formatting code. Jan 18, 2017
ea_redo_inv.m Formatting code. Jan 18, 2017
ea_reformat_isomatrix.m Merge Unilateral Lead Support, thanks to @QRabbani Jul 17, 2016
ea_regressout.m Fixes for last commit. Oct 4, 2016
ea_resample_planes.m Major speed improvements in ea_manualreconstruction.. Feb 4, 2016
ea_resliceanat.m Fix error prompt in ea_assignpretra Dec 11, 2016
ea_run.m Auto adjust MR/CT modality if multiple patients have been selected. Feb 19, 2017
ea_run_cluster.m Further tweak connectome support on HPC Dec 27, 2016
ea_sample_cuboid.m Pot. fix mail TH Aug 25, 2016
ea_sample_slice.m Modified lead_group to include NBS and be a bit more logical. Jun 18, 2016
ea_save_reconstruction.m Compatibility with lead_group on new reco format Jun 13, 2016
ea_savejson.m Added some error messages. Mar 28, 2015
ea_savelcopts.m Also included lc options into machine-readeable options Jan 16, 2017
ea_seemscoregistered.m CT is being tonemapped also for small coregcheck figs now. Dec 26, 2016
ea_setpath.m Fix in setpath Dec 15, 2016
ea_settransparency.m Transparency update Feb 2, 2017
ea_show_ctcoregistration.m Forgotten not Dec 26, 2016
ea_show_light.m Update Lightbulbs Jan 31, 2017
ea_show_normalization.m Show normalization now also showing (tonemapped) postop_ct Feb 19, 2017
ea_showatlas.m tag color buttons and update ea_keepatlaslabels Feb 20, 2017
ea_showcortex.m catch if template cortex doesn't exist Jan 30, 2017
ea_showcorticalstrip.m Fix in viz for lead_group Jan 22, 2017
ea_showdis.m Added Manual, next try Jun 24, 2014
ea_showelectrode.m Small fixes for lead-group and assoc. scripts Feb 19, 2017
ea_showfibres_volume.m Fix macaquemodus as reported by ramina Feb 11, 2017
ea_showisovolume.m Small fixes for lead-group and assoc. scripts Feb 19, 2017
ea_shownormsettings.m Added settings button to normalization functions Aug 17, 2016
ea_smooth_significance.m Merge pull request #67 from QRabbani/master Jul 13, 2016
ea_space.m Updates to mapper & spaces Feb 13, 2017
ea_spec2dwrite.fig Now you can also show native space cut views. Jan 11, 2017
ea_spec2dwrite.m Fix 2D output Feb 14, 2017
ea_spec_atlas.m Fix VTA visualization with new sliders Feb 12, 2017
ea_spm_applytransforms.m added resize_img function which was somehow missing. Jan 16, 2017
ea_stimparams.fig Fixed k11 impedance issue as reported by ak May 29, 2016
ea_stimparams.m Progress in VAT-model Dec 15, 2016
ea_storemachineprefs.m Added switch space to manu Jan 16, 2017
ea_tdhandles2options.m 2d writeout now working, too Jan 16, 2017
ea_tonemap_ct.m CT is being tonemapped also for small coregcheck figs now. Dec 26, 2016
ea_tonemapct_file.m Can now generate checkregfiles from Menu, too Dec 27, 2016
ea_ttest.m Added Manual, next try Jun 24, 2014
ea_update.m Check dir existence before mkdir during updating. Jan 13, 2017
ea_update_data.m Check dir existence before mkdir during updating. Jan 13, 2017
ea_updaterecentpatients.m Added standalone-mode for lead_connectome Jul 23, 2016
ea_viz2brainbrowser.m Fixed lead-server support for ML>2014b graphics. Nov 29, 2015
ea_whichnormmethod.m Now atlases and labeling files may be imported from other spaces via … Jan 22, 2017
ea_write.m Drop saving lead scene as matlab figure. Feb 1, 2017
ea_write_fiducials.m Added Manual, next try Jun 24, 2014
ea_writeplanes.m Fix in ea_export for multiple patients Feb 14, 2017
lead.fig Rm lead_macaque from start GUI Jan 17, 2017
lead.m Slices now report mm back Feb 7, 2017
lead_anatomy.fig Added FSL slicer functionality to Lead-DBS and Lead-Connectome Nov 2, 2016
lead_anatomy.m Boost startup speed of all lead apps Feb 8, 2017
lead_dbs.fig Changed order/hierarchy of MNI space and Atlas popups Jan 12, 2017
lead_dbs.m Let manual be available in macaque mode. Feb 15, 2017
lead_group.fig Added ability to mirror sides and better visualize isovolumes Dec 21, 2016
lead_group.m Fix 2D output Feb 14, 2017

README.md

LEAD-DBS

LEAD-DBS is NOT intended for clinical use!

About Lead-DBS

LEAD-DBS is a MATLAB-toolbox facilitating the:

  • reconstruction of deep-brain-stimulation (DBS) electrodes in the human brain on basis of postoperative MRI and/or CT imaging
  • the visualization of localization results in 2D/3D
  • a group-analysis of DBS-electrode placement results and their effects on clinical results
  • simulation of DBS stimulations (calculation of volume of activated tissue – VAT)
  • diffusion tensor imaging (DTI) based connectivity estimates and fiber-tracking from the VAT to other brain regions (connectomic surgery)

LEAD-DBS builds on SPM8/12, especially regarding warping and segmentation procedures.

Installation

Usually, Lead-DBS can be downloaded from our website (www.lead-dbs.org) in fully functional form. Alternatively, especially in case you wish to modify and contribute to Lead-DBS, you can

  • Clone the Lead-DBS repository from here.
  • Download the necessary datafiles using this link and unzip the downloaded folder into the cloned git repository.
  • We’d love to implement your improvements into Lead-DBS – please contact us for direct push access to Github or feel free to add pull-requests to the Lead-DBS repository.