8	./2D/make_2d_images.m
5	./2D/register_1d_images_set.m
4	./2D/make_synthetic_object.m
8	./2D/register_2d_images.m
5	./2D/make_2d_bump.m
31	./2D
47	./Bin/build_1d_bump_model_1.m
2	./Bin/apply_noise_to_points.m
2	./Bin/apply_noise_to_points.m~
52	./Bin
1	./MDoc/layout/template.html
4	./MDoc/layout/itemplate.html
6	./MDoc/layout
1	./MDoc/include/ocamaweblink.html
2	./MDoc/include
2	./MDoc/makehtml.m
3	./MDoc/makefig.m
1	./MDoc/doctool.m
1	./MDoc/document_aart.m
3	./MDoc/depgraph.m
3	./MDoc/genhtml.m
2	./MDoc/graphlayout.m
9	./MDoc/AART.fig
2	./MDoc/drawlayout.m
35	./MDoc
3	./Davies/nmi.m
3	./Davies/mi_davies.m
7	./Davies
2	./Helper/msd.m
2	./Helper/get_parameters_from_user.m
2	./Helper/perturb_points.m
2	./Helper/perturb_points_cps.m
2	./Helper/normalise_to_bounds.m
2	./Helper/gaussian_smooth.m
2	./Helper/is_invalid.m
2	./Helper/get_parameters_from_user.m~
2	./Helper/average_smooth.m
2	./Helper/cps_warp_1d.m
3	./Helper/linear_warp.m
2	./Helper/find_linear_warp.m
2	./Helper/discrepancy_image_1d.m
3	./Helper/poor_linear_warp.m
2	./Helper/show_mesh.m
3	./Helper/find_target_warp.m
3	./Helper/find_target_warp.m~
2	./Helper/apply_perturbation_to_points.m~
2	./Helper/apply_perturbation_to_points.m
43	./Helper
4	./Build/build_model.m
3	./Build/build_model_from_models.m
1	./Build/compute_wavelet.m~
4	./Build/compute_pdf.m
3	./Build/build_and_eval_model.m
2	./Build/compute_wavelet.m
18	./Build
2	./Model/measure_model_msd.m~
4	./Model/find_specificity.m
2	./Model/construct_model_example.m
3	./Model/measure_model.m
3	./Model/find_generalisability.m
3	./Model/show_shape_model.m
1	./Model/measure_wavelet.m~
2	./Model/measure_wavelet.m
4	./Model/show_combined_model.m
3	./Model/show_intensity_model.m
2	./Model/measure_pdf.m
2	./Model/test_examples.m
2	./Model/measure_pdf.m.back
2	./Model/measure_model_msd.m
3	./Model/make_combined_model.m
4	./Model/measure_model.m~
2	./Model/show_spec_v_modes.m
45	./Model
1	./Tests/grid_test.m
3	./Tests/test2.m
1	./Tests/test3.m
1	./Tests/test4.m
1	./Tests/test5.m
2	./Tests/test.m
1	./Tests/bump_test.m
1	./Tests/green_test.m
12	./Tests
27	./Tools/fontpicker.m
112	./Tools/fontpicker.fig
140	./Tools
1	./Evaluation/eval_model_cps_warp.m
1	./Evaluation/eval_model_cps_warp.m~
2	./Evaluation/eval_msd_linear_warp.m
3	./Evaluation/eval_groupwise_single_point.m
3	./Evaluation/eval_nmi_cps_warp.m
2	./Evaluation/eval_wavelet_multi_point.m
3	./Evaluation/eval_msd_cps_warp.m
3	./Evaluation/eval_nmi_multi_warp.m
3	./Evaluation/eval_msd_multi_warp.m
2	./Evaluation/eval_groupwise_multi_point.m
3	./Evaluation/eval_wavelet_single_point.m
3	./Evaluation/eval_mi_multi_warp.m
3	./Evaluation/eval_mi_cps_warp.m
1	./Evaluation/eval_model_multi_warp.m
2	./Evaluation/eval_msd.m
36	./Evaluation
3	./Repository/NRR/test_pushme_pullyou.m
1	./Repository/NRR/hist_entropy.m
4	./Repository/NRR/OJtest.m
1	./Repository/NRR/edges_from_triangulation.m
3	./Repository/NRR/objective_function.m
3	./Repository/NRR/pick_skull_points.m
2	./Repository/NRR/plot_surf.m
1	./Repository/NRR/interlace.m
2	./Repository/NRR/test_affine_trans.m
3	./Repository/NRR/OJshape.m
1	./Repository/NRR/README
1	./Repository/NRR/normalise_image.m
3	./Repository/NRR/OJtest2.m
6	./Repository/NRR/vent_stuff.m
2	./Repository/NRR/inverse_affine_trans.m
2	./Repository/NRR/eval_affine_objective_function.m
5	./Repository/NRR/test_stuff.m
1	./Repository/NRR/discrepancy_image.m
5	./Repository/NRR/nrr_registration.m
1	./Repository/NRR/test_scale_image.m
2	./Repository/NRR/nrr_trans.m
5	./Repository/NRR/test_disc.m
3	./Repository/NRR/demo_various_splines.m
2	./Repository/NRR/test_nrr_warps.m
4	./Repository/NRR/ani_warp.m
7	./Repository/NRR/register2.m
3	./Repository/NRR/affine_registration.m
1	./Repository/NRR/pull_back.m
2	./Repository/NRR/reg_params.m
3	./Repository/NRR/eval_nrr_objective_function.m
4	./Repository/NRR/green.m
1	./Repository/NRR/image_preprocessing.m
1	./Repository/NRR/calc_MML.m
4	./Repository/NRR/region_of_interest.m
1	./Repository/NRR/get_weights.m
2	./Repository/NRR/reg_params2.m
1	./Repository/NRR/push_forward.m
1	./Repository/NRR/mad_pixel_fuck.m
2	./Repository/NRR/scale_image.m
2	./Repository/NRR/affine_trans.m
7	./Repository/NRR/test_stuff2.m
7	./Repository/NRR/register.m
6	./Repository/NRR/pick_disc_points.m
2	./Repository/NRR/warpy_entropy_test.m
125	./Repository/NRR
2	./Repository/Stats/st_post_mal.m
1	./Repository/Stats/Contents.m
1	./Repository/Stats/st_sweep.m
6	./Repository/Stats/st_robustpca.m
5	./Repository/Stats/st_nanmvnorm.m
10	./Repository/Stats/st_impute.m
3	./Repository/Stats/st_eig.m
9	./Repository/Stats/st_incremental_pca.m
2	./Repository/Stats/st_mah.m
4	./Repository/Stats/st_pca.m
2	./Repository/Stats/st_nancov.c
1	./Repository/Stats/st_nancov.m
1	./Repository/Stats/st_nanmean.m
2	./Repository/Stats/st_pre_mal.m
50	./Repository/Stats
2	./Repository/Utils/u_convertpointstoradial.m
2	./Repository/Utils/u_gplot.m
2	./Repository/Utils/u_loadmarkedimagelist.m
3	./Repository/Utils/u_suptitle.m
14	./Repository/Utils/u_roipoly.cxx
2	./Repository/Utils/u_interpimage.m
2	./Repository/Utils/u_loadSMDpoints.m
4	./Repository/Utils/u_parsePartsfile.m
3	./Repository/Utils/Contents.m
2	./Repository/Utils/u_gridnd.m
2	./Repository/Utils/u_createsequencelist.m
3	./Repository/Utils/u_sphere_tesselation.m
2	./Repository/Utils/u_readParameter.m
4	./Repository/Utils/u_dijkstra.m
3	./Repository/Utils/u_newfunction.m
2	./Repository/Utils/readanalyze.m
4	./Repository/Utils/readheader.m
2	./Repository/Utils/saveheader.m
1	./Repository/Utils/u_roipoly.m
5	./Repository/Utils/u_packargs.m
1	./Repository/Utils/u_ensure_filesep_terminated.m
3	./Repository/Utils/makeheader.m
1	./Repository/Utils/readoneslice.m
2	./Repository/Utils/u_getimage.m
2	./Repository/Utils/u_parsePTSfile.m
1	./Repository/Utils/u_mirrormarkedimage.m
2	./Repository/Utils/u_defaultparams.m
2	./Repository/Utils/u_convertradialpoints.m
2	./Repository/Utils/u_saveframes.m
1	./Repository/Utils/u_savePTSfile.m
1	./Repository/Utils/u_partsGraph.m
2	./Repository/Utils/u_imread.m
7	./Repository/Utils/u_parseSMDfile.m
2	./Repository/Utils/writeanalyze.m
6	./Repository/Utils/u_gaussimagepyramid.m
100	./Repository/Utils
2	./Repository/Models/tools/private/plot_points.m
3	./Repository/Models/tools/private
1	./Repository/Models/tools/m_tool_show_search.m
4	./Repository/Models/tools/m_tool_interact_pdm.m
1	./Repository/Models/tools/interact.res
3	./Repository/Models/tools/m_tool_showapm.m
3	./Repository/Models/tools/m_tool_showpdm.m
2	./Repository/Models/tools/m_tool_showpfm.m
18	./Repository/Models/tools
2	./Repository/Models/@sphere_param/sphere_param.m
1	./Repository/Models/@sphere_param/get.m
2	./Repository/Models/@sphere_param/random_cauchy_params.m
1	./Repository/Models/@sphere_param/apply_param.m
2	./Repository/Models/@sphere_param/add_cauchy.m
9	./Repository/Models/@sphere_param
3	./Repository/Models/@m_tps_warper/shape_free_sample.m
4	./Repository/Models/@m_tps_warper/warped_instance.m
3	./Repository/Models/@m_tps_warper/shape_normalise.m
1	./Repository/Models/@m_tps_warper/subsref.m
2	./Repository/Models/@m_tps_warper/m_tps_warper.m
14	./Repository/Models/@m_tps_warper
2	./Repository/Models/@line_param/est_error.m
1	./Repository/Models/@line_param/display.m
1	./Repository/Models/@line_param/get.m
1	./Repository/Models/@line_param/set.m
1	./Repository/Models/@line_param/double.m
2	./Repository/Models/@line_param/line_param.m
1	./Repository/Models/@line_param/random_cauchy_params.m
2	./Repository/Models/@line_param/apply_param.m
1	./Repository/Models/@line_param/add_cauchy.m
13	./Repository/Models/@line_param
3	./Repository/Models/@m_delaunay_warper/shape_free_sample.m
5	./Repository/Models/@m_delaunay_warper/m_delaunay_warper.m
5	./Repository/Models/@m_delaunay_warper/warped_instance.m
6	./Repository/Models/@m_delaunay_warper/shape_normalise.m
1	./Repository/Models/@m_delaunay_warper/subsref.m
21	./Repository/Models/@m_delaunay_warper
3	./Repository/Models/@m_slice_3d_warper/shape_free_sample.m
1	./Repository/Models/@m_slice_3d_warper/warped_instance.m
2	./Repository/Models/@m_slice_3d_warper/m_slice_3d_warper.m
1	./Repository/Models/@m_slice_3d_warper/subsref.m
8	./Repository/Models/@m_slice_3d_warper
5	./Repository/Models/private/m_transform_corrs.m
4	./Repository/Models/private/m_incident_tri.c
1	./Repository/Models/private/m_incident_tri.m
2	./Repository/Models/private/m_fv2tri.m
3	./Repository/Models/private/m_nearest_pt.c
1	./Repository/Models/private/m_nearest_pt.m
17	./Repository/Models/private
1	./Repository/Models/@circle_param/display.m
1	./Repository/Models/@circle_param/circle_param.m
1	./Repository/Models/@circle_param/random_cauchy_params.m
2	./Repository/Models/@circle_param/apply_param.m
1	./Repository/Models/@circle_param/add_cauchy.m
7	./Repository/Models/@circle_param
2	./Repository/Models/m_asminstance.m
1	./Repository/Models/m_asmnormaliseProfiles.m
3	./Repository/Models/m_kotcheff_objective_function.m
1	./Repository/Models/m_txminstance.m
1	./Repository/Models/m_asmparams.m
5	./Repository/Models/m_asmsampleProfiles.m
1	./Repository/Models/m_denormaliseimage.m
4	./Repository/Models/Contents.m
2	./Repository/Models/m_mraamsearch.m
16	./Repository/Models/m_pdmparams.m
22	./Repository/Models/m_autolandmark.m
2	./Repository/Models/m_txmparams.m
8	./Repository/Models/m_asmsearch.m
1	./Repository/Models/m_smparams.m
2	./Repository/Models/m_apmstoim.m
2	./Repository/Models/m_asmpartNormals.m
2	./Repository/Models/m_normaliseimages.m
2	./Repository/Models/m_apmparams.m
1	./Repository/Models/m_pdminstance.m
10	./Repository/Models/m_trainaamfromdata.m
3	./Repository/Models/m_trainsm.m
8	./Repository/Models/m_trainapm.m
2	./Repository/Models/m_trainasm.m
1	./Repository/Models/m_normaliseimage.m
4	./Repository/Models/m_apminstance.m
9	./Repository/Models/m_asmsearchProfiles.m
4	./Repository/Models/m_trainpdm.m
8	./Repository/Models/m_trainpfm.m
5	./Repository/Models/m_traintxm.m
1	./Repository/Models/m_pfminstance.m
2	./Repository/Models/m_trainmraam.m
2	./Repository/Models/m_trainmrapm.m
7	./Repository/Models/m_aamsearch.m
2	./Repository/Models/m_pfmparams.m
1	./Repository/Models/m_sminstance.m
7	./Repository/Models/m_mdl_objective_function.m
2	./Repository/Models/m_apmreconstruct.m
265	./Repository/Models
541	./Repository
2	./Marsland/minka.m
2	./Marsland/nrr_trans_1d.m
2	./Marsland/green_1d.m
7	./Marsland
1	./Stamping/get_month.m
1	./Stamping/get_ip.m~
1	./Stamping/get_host.m
1	./Stamping/get_ip.m
1	./Stamping/get_year.m
1	./Stamping/get_year.m~
1	./Stamping/get_version.m
1	./Stamping/get_domain.m
1	./Stamping/get_month.m~
1	./Stamping/get_date.m
1	./Stamping/get_version.m.bck
1	./Stamping/get_month.m.bck
1	./Stamping/add_html_headers.m
14	./Stamping
13	./Simple_1D/build_1d_model.m
4	./Simple_1D/make_1d_images.m
2	./Simple_1D/run_model_opt.m
20	./Simple_1D
8	./Progress/progressbar.m
2	./Progress/gui_active.m
35	./Progress/gauge_abort_icon.mat
46	./Progress
5	./Optimise/optimise_all_warps_model.m
4	./Optimise/optimise_warps_msd.m
4	./Optimise/optimise_warps_nmi.m
4	./Optimise/optimise_warps.m
4	./Optimise/optimise_all_warps_mi.m
4	./Optimise/optimise_warps_mi.m
4	./Optimise/optimise_wavelet.m
4	./Optimise/optimise_all_warps_msd.m
4	./Optimise/optimise_all_warps_nmi.m
5	./Optimise/optimise_groupwise.m
5	./Optimise/optimise_warps_model.m
4	./Optimise/optimise_all_warps_model.m~
52	./Optimise
7	./Redundancy/build_1d_model_2_bump.m
3	./Redundancy/eval_mi_cps_warp(kate).m
11	./Redundancy
4	./Evaluate_Objective/eval_obj_fn_to_mean_surf.m
19	./Evaluate_Objective/eval_1d_app_model_obj_fn.m
4	./Evaluate_Objective/eval_obj_fn_to_mean.m
28	./Evaluate_Objective
4	./Graphics/.xvpics/background.jpg
3	./Graphics/.xvpics/aarttitle.gif
3	./Graphics/.xvpics/aarttitle.jpg
3	./Graphics/.xvpics/aarttitle.tif
4	./Graphics/.xvpics/aartlrg.jpg
4	./Graphics/.xvpics/aartlrg.tif
5	./Graphics/.xvpics/backgroundlarge.jpg
3	./Graphics/.xvpics/aart_title.tif
3	./Graphics/.xvpics/aart_title
4	./Graphics/.xvpics/isbe.tif
3	./Graphics/.xvpics/aartsm.tif
4	./Graphics/.xvpics/samples.tif
44	./Graphics/.xvpics
7	./Graphics/background.jpg
12	./Graphics/aarttitle.jpg
5	./Graphics/aartlrg.jpg
23	./Graphics/backgroundlarge.jpg
4	./Graphics/isbe.tif
3	./Graphics/aartsm.tif
27	./Graphics/samples.tif
126	./Graphics
1	./Twining/MI_test_oneD .m
2	./Twining/mi.m
4	./Twining
1	./Irrelevant/show_n_brains.m
1	./Irrelevant/show_brain_and_pts.m
3	./Irrelevant
11	./Callbacks/automation.m
11	./Callbacks/automation.m~
128	./Callbacks/register.m
120	./Callbacks/register.m~
8	./Callbacks/perturb.m
9	./Callbacks/perturb.m~
12	./Callbacks/advanced.m
11	./Callbacks/advanced.m~
4	./Callbacks/splash.m
315	./Callbacks
81	./Registration/build_1d_bump_model.m
81	./Registration/build_1d_bump_model.m~
5	./Registration/make_1d_bump.m
4	./Registration/setup_grid.m
172	./Registration
1	./path.m
1	./AART.m
12	./Functions_Listing.txt
65	./Figures/advanced.fig
60	./Figures/automation.fig
53	./Figures/perturb.fig
392	./Figures/register.fig
49	./Figures/splash.fig
620	./Figures
2393	.