Merge pull request #53 from Donders-Institute/development

Merge integrated pull from development branch
Donders-Institute · Sep 30, 2024 · d3886f7 · d3886f7
2 parents f3f9639 + 98337c2
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diff --git a/README.md b/README.md
diff --git a/configs/default_config.yaml b/configs/default_config.yaml
diff --git a/configs/tutorial_config.yaml b/configs/tutorial_config.yaml
diff --git a/examples/ROI_intersection.m b/examples/ROI_intersection.m
diff --git a/examples/calibration_bob_ventral_striatum.m b/examples/calibration_bob_ventral_striatum.m
diff --git a/examples/calibration_sjoerd.m b/examples/calibration_sjoerd.m
diff --git a/examples/example_batch_processing.m b/examples/example_batch_processing.m
diff --git a/examples/example_itrusst.m b/examples/example_itrusst.m
diff --git a/examples/example_morteza.m b/examples/example_morteza.m
diff --git a/examples/example_pipeline_judith.m b/examples/example_pipeline_judith.m
diff --git a/examples/example_plot_group_data_in_MNI.m b/examples/example_plot_group_data_in_MNI.m
diff --git a/examples/pipeline_bob_transducer_positioning.m b/examples/pipeline_bob_transducer_positioning.m
diff --git a/examples/pipeline_camila.m b/examples/pipeline_camila.m
diff --git a/examples/pipeline_sjoerd.m b/examples/pipeline_sjoerd.m
diff --git a/examples/pipeline_sjoerd_080922.m b/examples/pipeline_sjoerd_080922.m
diff --git a/examples/postprocessing_sjoerd.R b/examples/postprocessing_sjoerd.R
diff --git a/examples/postprocessing_sjoerd.m b/examples/postprocessing_sjoerd.m
diff --git a/functions/align_to_focus_axis_and_scale.m b/functions/align_to_focus_axis_and_scale.m
diff --git a/functions/analyze_transducer_position.m b/functions/analyze_transducer_position.m
diff --git a/functions/analyze_transducer_position_fast.m b/functions/analyze_transducer_position_fast.m
diff --git a/functions/bounded_interp1.m b/functions/bounded_interp1.m
diff --git a/functions/check_thermal_parameters.m b/functions/check_thermal_parameters.m
diff --git a/functions/combine_plots_by_suffix.m b/functions/combine_plots_by_suffix.m
diff --git a/functions/confirm_overwriting.m b/functions/confirm_overwriting.m
diff --git a/functions/confirmation_dlg.m b/functions/confirmation_dlg.m
diff --git a/functions/convert_final_to_MNI_matlab.m b/functions/convert_final_to_MNI_matlab.m
diff --git a/functions/convert_final_to_MNI_simnibs.m b/functions/convert_final_to_MNI_simnibs.m
diff --git a/functions/create_group_MNI_plots.m b/functions/create_group_MNI_plots.m
diff --git a/functions/find_min_factor.m b/functions/find_min_factor.m
diff --git a/functions/fitPowerLawParamsMulti.m b/functions/fitPowerLawParamsMulti.m
diff --git a/functions/getArc.m b/functions/getArc.m
diff --git a/functions/get_alpha_coeff.m b/functions/get_alpha_coeff.m
diff --git a/functions/get_crop_dims.m b/functions/get_crop_dims.m
diff --git a/functions/get_slice_by_label.m b/functions/get_slice_by_label.m
diff --git a/functions/get_trans_pos_from_trigger_markers.m b/functions/get_trans_pos_from_trigger_markers.m
diff --git a/functions/get_transducer_box.m b/functions/get_transducer_box.m
diff --git a/functions/get_xyz_mesh.m b/functions/get_xyz_mesh.m
diff --git a/functions/load_parameters.m b/functions/load_parameters.m
diff --git a/functions/masked_max_3d.m b/functions/masked_max_3d.m
diff --git a/functions/median_montage.m b/functions/median_montage.m
diff --git a/functions/mergeStructure.m b/functions/mergeStructure.m
diff --git a/functions/mni2subject_coords_LDfix.m b/functions/mni2subject_coords_LDfix.m
diff --git a/functions/phase_optimization_annulus.m b/functions/phase_optimization_annulus.m
diff --git a/functions/plot_coronal_slices.m b/functions/plot_coronal_slices.m
diff --git a/functions/plot_heating_sims.m b/functions/plot_heating_sims.m
diff --git a/functions/plot_isppa_over_image.m b/functions/plot_isppa_over_image.m
diff --git a/functions/plot_isppa_over_image_2d.m b/functions/plot_isppa_over_image_2d.m
diff --git a/functions/plot_t1_with_transducer.m b/functions/plot_t1_with_transducer.m
diff --git a/functions/position_transducer_localite.m b/functions/position_transducer_localite.m
diff --git a/functions/preprocess_brain.m b/functions/preprocess_brain.m
diff --git a/functions/prova.m b/functions/prova.m
diff --git a/functions/ras_to_grid.m b/functions/ras_to_grid.m
diff --git a/functions/round_if_integer.m b/functions/round_if_integer.m
diff --git a/functions/run_heating_simulations.m b/functions/run_heating_simulations.m
diff --git a/functions/run_segmentation.m b/functions/run_segmentation.m
diff --git a/functions/run_simulations.m b/functions/run_simulations.m
diff --git a/functions/setup_grid_source_sensor.m b/functions/setup_grid_source_sensor.m
diff --git a/functions/setup_medium.m b/functions/setup_medium.m
diff --git a/functions/setup_source.m b/functions/setup_source.m
diff --git a/functions/show_3d_head.m b/functions/show_3d_head.m
diff --git a/functions/show_positioning_plots.m b/functions/show_positioning_plots.m
diff --git a/functions/single_subject_pipeline_with_qsub.m b/functions/single_subject_pipeline_with_qsub.m
diff --git a/functions/smooth_img.m b/functions/smooth_img.m
diff --git a/functions/subset_fields.m b/functions/subset_fields.m
diff --git a/functions/transducer_setup.m b/functions/transducer_setup.m
diff --git a/functions/upsample_to_grid.m b/functions/upsample_to_grid.m
diff --git a/functions/zip_fields.m b/functions/zip_fields.m
diff --git a/single_subject_pipeline.m b/single_subject_pipeline.m
diff --git a/toolboxes/FEX-minimize b/toolboxes/FEX-minimize
diff --git a/toolboxes/FEX-minimize/.gitignore b/toolboxes/FEX-minimize/.gitignore
diff --git a/toolboxes/FEX-minimize/BUGS.m b/toolboxes/FEX-minimize/BUGS.m
diff --git a/toolboxes/FEX-minimize/README.md b/toolboxes/FEX-minimize/README.md