Lead-DBS is a MATLAB-toolbox facilitating deep brain stimulation electrode locations and connectomic imaging.
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Lead_manual rm doc images Jun 2, 2017
classes Fix color pointcloud function. Nov 29, 2018
cluster Consistent naming of UUID. Aug 2, 2018
common Allow to build upon preexisting ANTs warps. Dec 29, 2018
connectomics Clean up in 'ea_showdiscfibers'. Jan 17, 2019
dbshub Fixes for last commit. Oct 4, 2016
dependency 'ea_pdist2' calculates euclidean distance by default (same as 'pdist2'). Aug 1, 2017
dev Make old corrplot function produce square plots by default, too. Dec 5, 2018
ext_libs Added feature to hand-draw refine normalizations. Jan 16, 2019
helpers Add function to plot standalone colorbar. Jan 17, 2019
icons Update icons. Nov 8, 2018
legacy Fix coreg error due to change in 'ea_spm_coreg'. Aug 5, 2018
ls Commit after cortona. Nov 6, 2014
predict Added cortexcb 1 mm mask. Jan 16, 2019
support_scripts Show subject index during 'cs_dmri_conseed' in 'lead mapper'. Feb 1, 2018
templates Generalized possibility to include segmentations for ANTs based norms. Jan 14, 2019
toolbox Fix in magetnorm method Apr 19, 2018
tools Fix transmitting usercredentials and pseudonym for server upload. Dec 6, 2018
vatmodel Fix loading electrode model. May 7, 2018
.gitignore Add 'connectomes' folder to .gitignore Dec 21, 2017
.version.txt v2.1.8.1 Jan 2, 2019
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 Fix broken stimulation parameters after 'Prepare Stats'. Apr 17, 2018
ea_add_overlay.m Exp code on menu normalization. Jun 12, 2018
ea_add_overlay_singlefile.m Fix potential issue in 'ea_genatlastable'. Jan 19, 2018
ea_addnormmethods.m Major remodel of registration check workflow. Aug 28, 2017
ea_addobj.m Fix checking variables. Dec 6, 2018
ea_addrecentpatient.m Formatting. Jan 21, 2018
ea_addtsmask.m Clean tmp.nii from subcortical mask generation. Oct 17, 2018
ea_amendtoolboxoptions.m Fix 'normsetting' being overwritten in cluster or exported job. Aug 17, 2017
ea_anatomycontrol.fig Minor tweak of 'ea_anatomycontrol' figure. Apr 18, 2017
ea_anatomycontrol.m Further support for colored backdrops Jun 3, 2018
ea_anatomyslices.m Fixed visualization of RGB backdrops in elvis. Apr 26, 2018
ea_anatpreprocess.m Move ro/crop from DICOM import to anatpreprocess. Sep 13, 2018
ea_apply_coregistration.m Also accept flirtbbr matrices when using ea_apply_coregistration. Dec 9, 2018
ea_apply_normalization.m Remove legacy code from 'ea_apply_normalization'. Aug 6, 2018
ea_apply_normalization_tofile.m Added ANTs Option to process skulstripped images. Nov 29, 2018
ea_applyscrfmat.m Fix 'applyscrfmat' when only the 'R' electrode is selected. May 28, 2018
ea_assignbackdrop.m Tweak 2D setting window. Aug 7, 2018
ea_assignpretra.m Make sure segmentation volumes (STN/GPi/GPe/RN) go to end of presentf… Jan 12, 2019
ea_atlasselect.fig Tweak 'ea_atlasselect' UI. Sep 5, 2017
ea_atlasselect.m Further support for fibertract atlases. May 27, 2018
ea_autocoord.m Remove duplicate ea_assignpretra. Nov 29, 2018
ea_build_DTD.m Changed Diffusion Tensor to HARDI (elsewise misleading). Mar 17, 2016
ea_busyaction.m Added feature to hand-draw refine normalizations. Jan 16, 2019
ea_calc_distance.m Added Manual, next try Jun 24, 2014
ea_centralcomponent.m Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_centrality_significance.m Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_centroid.m Replaced imaging toolbox functions (edit 1) Aug 5, 2014
ea_checkcoreg.fig Tweak checkcoreg UI. Nov 21, 2018
ea_checkcoreg.m Fix matext for bbr. Dec 12, 2018
ea_checkctmrpresent.m Fix modality flag when no postop image is present. Aug 23, 2017
ea_checkfiles.m Formatting. Jun 6, 2017
ea_checkforwardinv.m Separate ea_detvoxsize function Jul 27, 2016
ea_checkinstall.m Formatting checkinstall list. May 3, 2018
ea_checkmacaque.m Added normalization to file to Tools menu Jan 15, 2017
ea_checkspm.m Updated checkspm to support new version format. Dec 4, 2017
ea_checkstructures.fig Added feature to hand-draw refine normalizations. Jan 16, 2019
ea_checkstructures.m Fixed issue with non-DISTAL STN atlas. Jan 17, 2019
ea_checktrajectsanity.m Added Manual, next try Jun 24, 2014
ea_compat_data.m Fix 'spacedefinitions' location. Aug 10, 2018
ea_compute_scrf.m Unify 'ea_coreg2images' function. Aug 8, 2018
ea_concatfv.m Fix FaceVertexCData dim. Nov 12, 2018
ea_concavehull.m Added Manual, next try Jun 24, 2014
ea_conncomp.m Changed ea_conncomp slightly. Aug 5, 2014
ea_coreg2images.m UI implementation of FSL BBR Dec 9, 2018
ea_coreg_all_mri.m Unify 'ea_coreg2images' function. Aug 8, 2018
ea_coreg_fa.m Fix 'ea_getptsoptions' for relative path. Oct 31, 2018
ea_coregctmri_ants.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregctmri_ants_multiple.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregctmri_ants_multiple_refine.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregctmri_ants_refine.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregctmri_brainsfit.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregctmri_brainsfit_multiple.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregmethod.m Move 'ea_resliceanat' calling into 'ea_anatpreprocess'. Apr 5, 2017
ea_coregmr.m UI implementation of FSL BBR Dec 9, 2018
ea_coregmr_ants.m Major remodel of registration check workflow. Aug 28, 2017
ea_coregmr_brainsfit.m Major remodel of registration check workflow. Aug 28, 2017
ea_coregmr_flirt.m Major remodel of registration check workflow. Aug 28, 2017
ea_coregmr_flirt_bbr.m UI implementation of FSL BBR Dec 9, 2018
ea_coregmr_spm.m Fix coreg error due to change in 'ea_spm_coreg'. Aug 5, 2018
ea_correctcoords.m Formatting. Oct 23, 2018
ea_corrplot_gen.m Make old corrplot function produce square plots by default, too. Dec 5, 2018
ea_cortexselect.fig cortex viewer update Nov 25, 2017
ea_cortexselect.m cortexsel update Feb 8, 2018
ea_create_tpm_darteltemplate.m Unify 'ea_coreg2images' function. Aug 8, 2018
ea_createatlascheck.m Largely enhanced checkstructures functionality. Dec 1, 2018
ea_credits.m Added many bugfixes, as well as DTI tracking functionally (using DTI&… Feb 7, 2015
ea_cylinder.m Merge pull request #67 from QRabbani/master Jul 13, 2016
ea_defaultoptions.m Much faster VTA mapper generation. Sep 13, 2017
ea_detect_edges_3d.m Ending with ea_dispercent 1 Aug 15, 2016
ea_detsides.m Compat fixes for multiple electrodes. Dec 4, 2018
ea_detstimname.m Sort the stimulation list by modified time in descending order. May 5, 2018
ea_detthresh.m Tweak 2D setting window. Aug 7, 2018
ea_dicm2nii.m Added dicm2nii as additional option to import Dicoms Nov 27, 2017
ea_dicom_import.m Move ro/crop from DICOM import to anatpreprocess. Sep 13, 2018
ea_discfiberssetting.fig Add discriminative fibers setting UI. Nov 15, 2018
ea_discfiberssetting.m Add discriminative fibers setting UI. Nov 15, 2018
ea_dispbn.m Formatting. Oct 23, 2018
ea_dispercent.m Fully incorporate FSL FLIRT and FNIRT Nov 14, 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 Fix color pointcloud function. Nov 29, 2018
ea_export.m Added gencode to map files between template and patient anchor space. Jun 12, 2018
ea_export_ls_index.m Commit after cortona. Nov 6, 2014
ea_export_server.m Fix vizstruct for exporting to json. Nov 12, 2018
ea_export_templates.m Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_exportfiducials.m Minor bug fixes to exporting fiducials and refine coords Apr 10, 2018
ea_exportisovolume.m Added functionality to run each ANTs stage on its own. However not wo… Jul 14, 2017
ea_exportvatmapping.m Updated statvat modeling scripts. Jan 16, 2018
ea_extrapol_coords.m Added Manual, next try Jun 24, 2014
ea_findcoords.m Added Manual, next try Jun 24, 2014
ea_findonemidpoint.m Formatting. Nov 17, 2017
ea_firstrun.m Added force ('f') flag to copyfile() to solve weird issue with Matlab… Feb 19, 2018
ea_firstrun_public.m Check dataset installation for github development version user. Aug 31, 2017
ea_fit_line.m Further dependency-reduction Jul 24, 2017
ea_genatlastable.m Fix display atlases in native space. Jan 4, 2019
ea_gencheckreg.m Fix missing 'leadprod' field. Mar 12, 2018
ea_gencheckregpair.m Fix gencheckregpair for weird filetype images. Dec 19, 2018
ea_gencheckregpair_deep.m Consistent naming of UUID. Aug 2, 2018
ea_gencontrastimage.m Add ea_delete helper function Nov 2, 2016
ea_gencoregcheckfigs.m Revised means to create statvat mappings. Jan 14, 2018
ea_gencoregcheckfigs_scrf.m Fix white space issue when executing external binaries under Windows. Aug 31, 2017
ea_genhdtrajectory.m Added Manual, next try Jun 24, 2014
ea_gentargetreport.m Removed M.stimparams throughout code (only exception left see issue #132 Dec 29, 2017
ea_genvat_dembek.m Included heuristic VTA-Model which can account for different pulse wi… May 3, 2018
ea_genvat_horn.m Fixed proper handling of rest_*.nii filenames in mapper. However this… Aug 17, 2018
ea_genvat_kuncel.m Fixed stimulation issue when calling from lead group Aug 9, 2017
ea_genvat_maedler.m Fixed stimulation issue when calling from lead group Aug 9, 2017
ea_get_icn.m Enable 'ea_get_icn' to control the size of the icon. Jun 2, 2017
ea_getearoot.m Small additions to get to standalone version Mar 6, 2017
ea_getfsstatesavedir.m option to save fibers in dev mode Mar 1, 2018
ea_getmagetpeers.m Storing normsettings in global machine prefs. Apr 15, 2017
ea_getnativemni.m ea_getnativemni.m defaults to min space Jan 30, 2017
ea_getpatients.m Added next and previous patient buttons to Lead-DBS GUI Aug 31, 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 Better handling of output folder in mapper if e.g. using .txt files. Dec 14, 2018
ea_hotfix.m Change hotfix menu to 'Install development version of Lead'. Feb 9, 2018
ea_hyperlink_label.m Add hyperlink label Jun 20, 2016
ea_imageclassifier.fig More robust imageclassifier. Aug 4, 2017
ea_imageclassifier.m Fix 'prefs.rest'. May 23, 2018
ea_importcorticalels.m import cortical els update Mar 30, 2017
ea_importfs.m update importfs Apr 8, 2018
ea_imshowpair.m coronar -> coronal Jun 12, 2018
ea_init_coregctpopup.m Major remodel of registration check workflow. Aug 28, 2017
ea_init_coregmrpopup.m Disable FSL BBR for now. Dec 22, 2018
ea_initrecentpatients.m Fixes to make standalone (more) possible Mar 19, 2017
ea_isosignificance.m Get rid of pdist dependency (stats toolbox) Jul 24, 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 Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_leoo_significance_weighteddist.m Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_linsolve.m Replaced linsolve with a non-shearing version. Aug 19, 2016
ea_listatlassets.m Fix native atlas listing. Aug 8, 2017
ea_load_reconstruction.m Amend Nov 10, 2018
ea_load_trajectory.m Consolidated newly introduced "site" back to "side" to avoid confusion. Dec 27, 2017
ea_magetcheck_norm_peers.m Fixed some MAGeT workflow issues. Apr 17, 2018
ea_mancor_updatecoords.m Switch to serial (one electrode at a time) reconstructions. Dec 27, 2017
ea_mancor_updatescene.m Fixed wrong scaling for BSCI-Leads in Native Space. Nov 15, 2018
ea_manualreconstruction.m Removed DiODe from developer mode. Dec 27, 2018
ea_map_coords.m UI implementation of FSL BBR Dec 9, 2018
ea_mapelmodel2reco.m chmod. May 24, 2018
ea_maximize.m Fully incorporate FSL FLIRT and FNIRT Nov 14, 2016
ea_menu_addtransfer.m Added some shortcuts to Menu items Apr 14, 2017
ea_methods.m # ANTs wrapper now writes out text file with the command ANTs used Apr 20, 2017
ea_methodsdisp.fig Show methods in small popup Mar 19, 2017
ea_methodsdisp.m More method dumps Mar 22, 2017
ea_mirrorsides.m Fix nonlinear mirroring of isomatrix values from variables in lead group Sep 26, 2017
ea_mod_tex.m Add toc to pdf export. Nov 13, 2018
ea_nanmean.m Further dependency-reduction Jul 24, 2017
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_niiVAT2fvVAT.m orientation for directional leads without nii_reslice Jan 29, 2018
ea_norm_ptspecific_atl.m Fix Umlaut text. May 28, 2018
ea_normal.m Update release. Dec 6, 2014
ea_normalize_ants.m Add ability to use fiducial helpers for normalizations. Jan 14, 2019
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 coronar -> coronal Jun 12, 2018
ea_normalize_maget.m Further fixes & formating in maget norm. Apr 24, 2018
ea_normalize_maget_segment.m Refine coregistration/normalization related function naming. Aug 6, 2018
ea_normalize_schoenecker.m coronar -> coronal Jun 12, 2018
ea_normalize_spmdartel.m coronar -> coronal Jun 12, 2018
ea_normalize_spmnewseg.m Added possibility to scale regularization parameters in SPM new Segment. Nov 29, 2018
ea_normalize_spmshoot.m coronar -> coronal Jun 12, 2018
ea_normalize_suit.m coronar -> coronal Jun 12, 2018
ea_normsettings_ants.fig Allow to build upon preexisting ANTs warps. Dec 29, 2018
ea_normsettings_ants.m Allow to build upon preexisting ANTs warps. Dec 29, 2018
ea_normsettings_fsl.fig normsetting UI minor tweak. Jul 18, 2017
ea_normsettings_fsl.m Fix title string for FSL normsetting. Jul 31, 2017
ea_normsettings_maget.fig Tweak MAGeT setting UI Aug 19, 2016
ea_normsettings_maget.m Storing normsettings in global machine prefs. Apr 15, 2017
ea_normsettings_maget_segment.fig Fixed some issues with MAGeT-like Segmentation. Apr 13, 2018
ea_normsettings_maget_segment.m Storing normsettings in global machine prefs. Apr 15, 2017
ea_normsettings_schoenecker.fig Also allow LEAD_groupanalysis.mat files to dnd onto lead group window. Sep 3, 2017
ea_normsettings_schoenecker.m Fix 'normsetting' being overwritten in cluster or exported job. Aug 17, 2017
ea_normsettings_spmnewseg.fig UI tweak. Nov 29, 2018
ea_normsettings_spmnewseg.m Added possibility to scale regularization parameters in SPM new Segment. Nov 29, 2018
ea_openin.m Fix "open in..." from lead group Nov 27, 2017
ea_options2handles.m Fix 'options.dicomimp' field. May 7, 2018
ea_options2tdhandles.m Updated atlasselect tool to show May 29, 2017
ea_orient_darkstar.m Minor Improvement to ea_orient Jan 22, 2018
ea_orient_intensitypeaksFFT.m Plugin for the automatic detection of directional lead rotation (base… Jan 5, 2018
ea_orient_intensitypeaksdirmarker.m Plugin for the automatic detection of directional lead rotation (base… Jan 5, 2018
ea_orient_intensityprofile.m Plugin for the automatic detection of directional lead rotation (base… Jan 5, 2018
ea_orient_interpimage.m Plugin for the automatic detection of directional lead rotation (base… Jan 5, 2018
ea_orient_main.m Layout DiODe Jan 10, 2019
ea_orient_respecifyslices.m Some more changes in ea_orient_main for Manual Refine Workflow. Apr 16, 2018
ea_orient_rollpitchyaw.m Plugin for the automatic detection of directional lead rotation (base… Jan 5, 2018
ea_precoreg.m ea_precoreg now works without calling spm_jobman and stores the trans… Feb 9, 2018
ea_prefs.m Consistent naming of UUID. Aug 2, 2018
ea_prepare_slice.m Formatting. Nov 17, 2017
ea_ptspecific_atl.m Fix potential issue in 'ea_genatlastable'. Jan 19, 2018
ea_rangesearch.m Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_rcpatientscallback.m Support dragndrop in lead anatomy and mapper UI. Aug 6, 2017
ea_read_fiducials.m Fix zooming of electrodes in 3D visualization. Aug 21, 2017
ea_reconstruct.m Formatting. Nov 5, 2017
ea_reconstruct_coords.m Further dependency-reduction Jul 24, 2017
ea_reconstruct_trajectory.m Minor change to TRAC/CORE error string to display patient ID to help … May 18, 2018
ea_reconstruction2acpc.m Fix 'Done' and time display after warping the coordinates. Mar 12, 2018
ea_reconstruction2mni.m Fix 'applyscrfmat' when only the 'R' electrode is selected. May 28, 2018
ea_reconstruction2native.m Fix 'applyscrfmat' when only the 'R' electrode is selected. May 28, 2018
ea_redo_inv.m Formatting code. Jan 18, 2017
ea_refinecoords.m Fix bug in refine coords method when using MRI. Dec 30, 2018
ea_reformat_isomatrix.m Merge Unilateral Lead Support, thanks to @QRabbani Jul 17, 2016
ea_refreshscrf.m Formatting. Mar 6, 2018
ea_regressout.m Fixes for last commit. Oct 4, 2016
ea_resample_planes.m Introducing "x-ray" mode for DBS localization Mar 17, 2018
ea_resliceanat.m 'ea_resliceanat' method switched to 'ResampleImageBySpacing'. Nov 21, 2018
ea_run.m Fix DICOM import in 'ea_autocoord'. Mar 12, 2018
ea_run_cluster.m Fix 'normsetting' being overwritten in cluster or exported job. Aug 17, 2017
ea_runmanual.m Replaced ancient ea_corrplot figure with gramm based simpler-interfac… Apr 4, 2018
ea_runmanualslicer.m Added option to reconstruct lead trajectory manually using slicer. In… May 21, 2018
ea_runpacer.m Clean PaCER integration Nov 15, 2018
ea_runslicer.m Fix runslicer for multiple patients case. Oct 26, 2018
ea_runtraccore.m Fix 'applyscrfmat' when only the 'R' electrode is selected. May 28, 2018
ea_sample_cuboid.m Get rid of pdist dependency (stats toolbox) Jul 24, 2017
ea_sample_slice.m Some compatibility for unilateral leads. Sep 4, 2017
ea_save_reconstruction.m Compat fixes for multiple electrodes. Dec 4, 2018
ea_save_trajectory.m Consolidated newly introduced "site" back to "side" to avoid confusion. Dec 27, 2017
ea_savejson.m Added some error messages. Mar 28, 2015
ea_savelcopts.m Fix 'normsetting' being overwritten in cluster or exported job. Aug 17, 2017
ea_seemscoregistered.m Fix 'ea_open_vol' for multi-vol image. Jan 29, 2018
ea_segment_electrode.m Refine trajectory toggle logic. Nov 8, 2018
ea_setpath.m Fix spm path for cluster run. Aug 23, 2017
ea_settransparency.m Transparency update Feb 2, 2017
ea_show_coregistration.m Fixed workflow details. Sep 12, 2018
ea_show_light.m Fix lighting of slices Feb 24, 2017
ea_show_normalization.m Minor change of the 'show normalization' window title. Aug 6, 2017
ea_showatlas.m Fix group toggle for unilateral/multiple/heterogenous electrode group. Nov 13, 2018
ea_showcortex.m update importfs Apr 8, 2018
ea_showcorticalstrip.m Changed further appearances of linsolve to mldivide Feb 24, 2017
ea_showdis.m Added Manual, next try Jun 24, 2014
ea_showelectrode.m Add Tag to electrode patches. Nov 13, 2018
ea_showfibres_volume.m Fix S structure for 'ea_showfibres_volume'. May 4, 2018
ea_showisovolume.m Integrate discriminative fibers setting into lead group. Nov 15, 2018
ea_shownormsettings.m Added settings button to normalization functions Aug 17, 2016
ea_smooth_significance.m 'ea_crop_nii_bb' also supports '.gz' image now. May 2, 2017
ea_space.m Fixed warning with appropriate suggestion to redownload data files. D… Apr 17, 2018
ea_spec2dwrite.fig Tweak 2D setting window. Aug 7, 2018
ea_spec2dwrite.m Tweak 2D setting window. Aug 7, 2018
ea_spec_atlas.m Fix VTA visualization with new sliders Feb 12, 2017
ea_spm_apply_coregistration.m Update comments for SPM and ANTs interpolation method. Aug 7, 2018
ea_spm_apply_normalization.m Refine coregistration/normalization related function naming. Aug 6, 2018
ea_spm_coreg.m Unify 'ea_coreg2images' function. Aug 8, 2018
ea_spm_dicom_import.m Fix overwritting issue during dcm2nii conversion using SPM. Aug 27, 2018
ea_stimparams.fig UI tweak Dec 25, 2017
ea_stimparams.m Fixes in lead group Jul 12, 2018
ea_storemachineprefs.m Added switch space to manu Jan 16, 2017
ea_storeupdatecortex.m cortex viewer complete v1 Feb 8, 2018
ea_subcorticalrefine.fig Add 'Open directory' buttons to 'checkcoreg' and 'subcorticalrefine' … Feb 22, 2018
ea_subcorticalrefine.m Avoid writing reconstruction twice during scrf. Oct 26, 2018
ea_tdhandles2options.m Fix 'normsetting' being overwritten in cluster or exported job. Aug 17, 2017
ea_textdisp.fig Fixed bug in slab detection Apr 4, 2017
ea_textdisp.m Added function to show processing report. Apr 4, 2017
ea_tightfig.m Dual view for single electrode manual reconstruction view. Jan 6, 2018
ea_tonemap_ct.m Further increase in contrast of albada tonemapping method. Oct 27, 2017
ea_tonemapct_file.m Added IR as GPi modality. Dec 26, 2018
ea_trk2ftr.m Fix transpose in trk2ftr. Nov 14, 2018
ea_ttest.m Added Manual, next try Jun 24, 2014
ea_update.m Fix false alert in 'ea_hotfix'. Mar 29, 2017
ea_update_data.m Check dir existence before mkdir during updating. Jan 13, 2017
ea_updatecortex.m cortex viewer complete v1 Feb 8, 2018
ea_updaterecentpatients.m Formatting. Jan 21, 2018
ea_vatsettings_dembek.fig Allow all pulse widths in Dembek VAT May 4, 2018
ea_vatsettings_dembek.m Allow all pulse widths in Dembek VAT May 4, 2018
ea_vatsettings_horn.fig Fix setting control in 'ea_stimparams'. Dec 3, 2017
ea_vatsettings_horn.m Put back in "general heuristic" e-field threshold as stated in Astrom… Sep 17, 2017
ea_viz2brainbrowser.m Fixed lead-server support for ML>2014b graphics. Nov 29, 2015
ea_whichnormmethod.m Fix 'ea_apply_normalization_tofile' for directory without filesep. Aug 6, 2017
ea_write.m Small UI fixes. Jul 20, 2018
ea_write_fiducials.m Added Manual, next try Jun 24, 2014
ea_writeplanes.m Added feature to hand-draw refine normalizations. Jan 16, 2019
lead.fig Rm lead_macaque from start GUI Jan 17, 2017
lead.m UI tweak. Dec 31, 2017
lead_anatomy.fig UI tweak. Dec 31, 2017
lead_anatomy.m Fix missing 'leadprod' field. Mar 12, 2018
lead_dbs.fig Increase electrode number up to 15. Oct 1, 2018
lead_dbs.m Increase electrode number up to 15. Oct 1, 2018
lead_group.fig Integrate discriminative fibers setting into lead group. Nov 15, 2018
lead_group.m Fix discfibers machine setting. Nov 29, 2018
lead_group_connectome.fig Added lead groupconnectome to main (export from dev). Jul 27, 2018
lead_group_connectome.m Fix fiber aggregation in lead_group_connectome. Aug 21, 2018
lead_predict.fig Tweak lead predict UI. May 24, 2018
lead_predict.m Added lead predict to main branch Mar 9, 2018

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.