├── .github ├── FUNDING.yml └── workflows │ ├── build.yml │ └── test.yml ├── .gitignore ├── FreeSurferColorLUT.txt ├── LICENSE ├── README.md ├── SliceModel.cpp ├── SliceModel.h ├── auto_track.cpp ├── auto_track.h ├── auto_track.ui ├── cmd ├── ana.cpp ├── atk.cpp ├── atl.cpp ├── cnn.cpp ├── cnt.cpp ├── exp.cpp ├── img.cpp ├── img.hpp ├── qc.cpp ├── rec.cpp ├── reg.cpp ├── ren.cpp ├── src.cpp ├── trk.cpp ├── vis.cpp └── xnat.cpp ├── connectometry ├── createdbdialog.cpp ├── createdbdialog.h ├── createdbdialog.ui ├── db_window.cpp ├── db_window.h ├── db_window.ui ├── group_connectometry.cpp ├── group_connectometry.hpp ├── group_connectometry.ui ├── group_connectometry_analysis.cpp ├── group_connectometry_analysis.h ├── match_db.cpp ├── match_db.h └── match_db.ui ├── console.cpp ├── console.h ├── console.ui ├── cuda ├── reg.cu ├── reg_cdm.cu └── reg_linear.cu ├── dicom ├── dicom_parser.cpp ├── dicom_parser.h ├── dicom_parser.ui ├── dwi_header.cpp └── dwi_header.hpp ├── dicom_tag.txt ├── dsi_studio.icns ├── dsi_studio.ico ├── dsi_studio.rc ├── icons.qrc ├── icons ├── 3view.xpm ├── add.xpm ├── add_surface.xpm ├── ajax-loader.gif ├── atlas.xpm ├── axial.xpm ├── ball.xpm ├── conn.xpm ├── console.xpm ├── coronal.xpm ├── cubic.xpm ├── curves.xpm ├── delete.xpm ├── down.xpm ├── dsi_studio.png ├── dwi.png ├── fib.png ├── fullscreen.xpm ├── guides.xpm ├── mosaic.xpm ├── move.xpm ├── new.xpm ├── open.xpm ├── poly.xpm ├── preferences.xpm ├── rec.xpm ├── red_cross.xpm ├── report.xpm ├── rgb.xpm ├── rotate.xpm ├── ruler.xpm ├── run.xpm ├── sag.xpm ├── save.xpm ├── save_all.xpm ├── slice.xpm ├── stat.xpm ├── stop.xpm ├── tractogram.png ├── tracts.xpm ├── up.xpm ├── zoom-in.xpm └── zoom-out.xpm ├── libs ├── dsi │ ├── basic_voxel.cpp │ ├── basic_voxel.hpp │ ├── dsi_interface_imp.cpp │ ├── dti_process.hpp │ ├── gqi_mni_reconstruction.hpp │ ├── gqi_process.cpp │ ├── gqi_process.hpp │ ├── hist_process.hpp │ ├── image_model.cpp │ ├── image_model.hpp │ ├── odf_process.hpp │ ├── tessellated_icosahedron.cpp │ └── tessellated_icosahedron.hpp ├── mapping │ ├── atlas.cpp │ ├── atlas.hpp │ ├── connectometry_db.cpp │ └── connectometry_db.hpp └── tracking │ ├── basic_process.hpp │ ├── fib_data.cpp │ ├── fib_data.hpp │ ├── roi.cpp │ ├── roi.hpp │ ├── tracking_method.hpp │ ├── tracking_thread.cpp │ ├── tracking_thread.hpp │ ├── tract_cluster.cpp │ ├── tract_cluster.hpp │ ├── tract_model.cpp │ └── tract_model.hpp ├── main.cpp ├── mainwindow.cpp ├── mainwindow.h ├── mainwindow.ui ├── manual_alignment.cpp ├── manual_alignment.h ├── manual_alignment.ui ├── opengl ├── glwidget.cpp ├── glwidget.h ├── region_render.cpp ├── region_render.hpp ├── renderingtablewidget.cpp ├── renderingtablewidget.h ├── tract_render.cpp └── tract_render.hpp ├── options.txt ├── other ├── LICENSE ├── color_map │ ├── COLOR_LICENSE │ ├── cividis.txt │ ├── inferno.txt │ ├── jet.txt │ ├── magma.txt │ ├── plasma.txt │ ├── tab10.txt │ ├── tab20.txt │ ├── tab20b.txt │ ├── tab20c.txt │ ├── twilight.txt │ └── viridis.txt ├── device.txt └── topup_param.txt ├── qcolorcombobox.cpp ├── qcolorcombobox.h ├── qcompletelineedit.cpp ├── qcompletelineedit.h ├── reconstruction ├── reconstruction_window.cpp ├── reconstruction_window.h └── reconstruction_window.ui ├── reg.hpp ├── regtoolbox.cpp ├── regtoolbox.h ├── regtoolbox.ui ├── resource.qrc ├── tracking ├── atlasdialog.cpp ├── atlasdialog.h ├── atlasdialog.ui ├── connectivity_matrix_dialog.cpp ├── connectivity_matrix_dialog.h ├── connectivity_matrix_dialog.ui ├── device.cpp ├── device.h ├── devicetablewidget.cpp ├── devicetablewidget.h ├── region │ ├── RegionModel.h │ ├── Regions.cpp │ ├── Regions.h │ ├── regiontablewidget.cpp │ └── regiontablewidget.h ├── slice_view_scene.cpp ├── slice_view_scene.h ├── tracking_window.cpp ├── tracking_window.h ├── tracking_window.ui ├── tracking_window_action.cpp ├── tract │ ├── tracttablewidget.cpp │ └── tracttablewidget.h ├── tract_report.cpp ├── tract_report.hpp └── tract_report.ui ├── view_image.cpp ├── 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