├── README.md ├── code ├── classes │ ├── @MrAffineGeometry │ │ ├── MrAffineGeometry.m │ │ ├── apply_inverse_transformation.m │ │ ├── apply_transformation.m │ │ ├── get_affine_matrix.m │ │ ├── load.m │ │ ├── load_par.m │ │ ├── set_from_dim_info.m │ │ ├── set_from_geometry4D.m │ │ ├── update.m │ │ └── update_from_affine_matrix.m │ ├── @MrCopyData │ │ ├── MrCopyData.m │ │ ├── clear.m │ │ ├── comp.m │ │ ├── copyobj.m │ │ ├── diffobj.m │ │ ├── find.m │ │ ├── get_nonempty_fields.m │ │ ├── get_properties_to_update.m │ │ ├── isequal.m │ │ ├── print.m │ │ ├── print_diff.m │ │ ├── read_struct_mat.m │ │ └── update_properties_from.m │ ├── @MrCopyDataTest │ │ └── MrCopyDataTest.m │ ├── @MrDataNd │ │ ├── MrDataNd.m │ │ ├── abs.m │ │ ├── angle.m │ │ ├── circshift.m │ │ ├── combine.m │ │ ├── conj.m │ │ ├── cumsum.m │ │ ├── diff.m │ │ ├── exp.m │ │ ├── fft.m │ │ ├── flip.m │ │ ├── fliplr.m │ │ ├── flipud.m │ │ ├── get_filename.m │ │ ├── hist.m │ │ ├── ifft.m │ │ ├── imag.m │ │ ├── image2k.m │ │ ├── isreal.m │ │ ├── k2image.m │ │ ├── load.m │ │ ├── log.m │ │ ├── max.m │ │ ├── maxip.m │ │ ├── mean.m │ │ ├── meanval.m │ │ ├── median.m │ │ ├── min.m │ │ ├── minip.m │ │ ├── minus.m │ │ ├── mod.m │ │ ├── ndims.m │ │ ├── perform_binary_operation.m │ │ ├── perform_unary_operation.m │ │ ├── plus.m │ │ ├── power.m │ │ ├── prctile.m │ │ ├── rdivide.m │ │ ├── read_cpx.m │ │ ├── read_matrix_from_workspace.m │ │ ├── read_nifti_analyze.m │ │ ├── read_par_rec.m │ │ ├── read_recon6_image_data.m │ │ ├── read_single_file.m │ │ ├── real.m │ │ ├── remove_dims.m │ │ ├── resize.m │ │ ├── rms.m │ │ ├── rmse.m │ │ ├── rot90.m │ │ ├── save.m │ │ ├── select.m │ │ ├── snr.m │ │ ├── split.m │ │ ├── sqrt.m │ │ ├── std.m │ │ ├── sum.m │ │ ├── times.m │ │ ├── unwrap.m │ │ ├── write_nifti_analyze.m │ │ ├── write_nifti_analyze_nd.m │ │ └── write_single_file.m │ ├── @MrDimInfo │ │ ├── MrDimInfo.m │ │ ├── add_dims.m │ │ ├── combine.m │ │ ├── get_default_dim_labels.m │ │ ├── get_default_dim_units.m │ │ ├── get_dims.m │ │ ├── get_geometry4D.m │ │ ├── get_non_singleton_dimensions.m │ │ ├── get_singleton_dimensions.m │ │ ├── index2label.m │ │ ├── index2sample.m │ │ ├── load.m │ │ ├── numArgumentsFromSubscript.m │ │ ├── permute.m │ │ ├── read_nifti.m │ │ ├── read_par.m │ │ ├── remove_dims.m │ │ ├── sample2index.m │ │ ├── select.m │ │ ├── set_dims.m │ │ ├── set_from_affine_geometry.m │ │ ├── set_from_filenames.m │ │ ├── set_from_geometry4D.m │ │ ├── split.m │ │ ├── subsasgn.m │ │ ├── subsref.m │ │ └── update_and_validate_properties_from.m │ ├── @MrGlm │ │ ├── MrGlm.m │ │ ├── get_matlabbatch.m │ │ ├── init_glm.m │ │ ├── matlabbatch │ │ │ └── mb_specify_1st_level.m │ │ ├── plot_design_matrix.m │ │ └── plot_regressors.m │ ├── @MrImage │ │ ├── MrImage.m │ │ ├── analyze_rois.m │ │ ├── append.m │ │ ├── apply_spm_method_on_many_4d_splits.m │ │ ├── apply_spm_method_per_4d_split.m │ │ ├── apply_threshold.m │ │ ├── binarize.m │ │ ├── cine.m │ │ ├── combine.m │ │ ├── combine_complex.m │ │ ├── compute_coeff_var.m │ │ ├── compute_diff_last_first.m │ │ ├── compute_mask.m │ │ ├── compute_roi_stats.m │ │ ├── compute_stat_image.m │ │ ├── create_empty_image.m │ │ ├── draw_mask.m │ │ ├── edge.m │ │ ├── extract_plot4D_data.m │ │ ├── extract_rois.m │ │ ├── imclose.m │ │ ├── imdilate.m │ │ ├── imerode.m │ │ ├── imfill.m │ │ ├── pca.m │ │ ├── permute.m │ │ ├── plot.m │ │ ├── plot3d.m │ │ ├── plot4D.m │ │ ├── plot_overlays.m │ │ ├── plot_rois.m │ │ ├── realign.m │ │ ├── recast_as_MrImageSpm4D.m │ │ ├── scale.m │ │ ├── select4D.m │ │ ├── set_filename.m │ │ ├── set_geometry_callback.m │ │ ├── smooth.m │ │ ├── split_complex.m │ │ ├── split_into_MrImageSpm4D.m │ │ ├── strip_slice.m │ │ └── update_geometry_dim_info.m │ ├── @MrImageGeometry │ │ ├── MrImageGeometry.m │ │ ├── apply_inverse_transformation.m │ │ ├── apply_transformation.m │ │ ├── convert.m │ │ ├── create_empty_image.m │ │ ├── diffobj.m │ │ ├── get_affine_matrix.m │ │ ├── load.m │ │ ├── load_par.m │ │ ├── permute.m │ │ ├── set_from_dimInfo_and_affineGeom.m │ │ ├── update.m │ │ └── update_from_affine_matrix.m │ ├── @MrImageSpm4D │ │ ├── MrImageSpm4D.m │ │ ├── apply_deformation_field.m │ │ ├── apply_realign.m │ │ ├── coregister_to.m │ │ ├── finish_processing_step.m │ │ ├── get_all_matlabbatch_methods.m │ │ ├── get_matlabbatch.m │ │ ├── init_processing_step.m │ │ ├── matlabbatch │ │ │ ├── mb_apply_transformation_field.m │ │ │ ├── mb_coregister_to.m │ │ │ ├── mb_realign.m │ │ │ ├── mb_reslice.m │ │ │ ├── mb_segment.m │ │ │ ├── mb_smooth.m │ │ │ └── mb_warp.m │ │ ├── realign.m │ │ ├── recast_as_MrImage.m │ │ ├── reslice.m │ │ ├── save.m │ │ ├── segment.m │ │ ├── smooth.m │ │ └── t_filter.m │ ├── @MrRoi │ │ ├── MrRoi.m │ │ ├── compute_stats.m │ │ ├── extract.m │ │ ├── load_data.m │ │ ├── plot.m │ │ └── save.m │ ├── @MrSeries │ │ ├── MrSeries.m │ │ ├── analyze_rois.m │ │ ├── compute_masks.m │ │ ├── compute_stat_images.m │ │ ├── compute_tissue_probability_maps.m │ │ ├── coregister.m │ │ ├── find_max_processing_step.m │ │ ├── finish_processing_step.m │ │ ├── get_all_image_objects.m │ │ ├── get_all_matlabbatch_methods.m │ │ ├── get_matlabbatch.m │ │ ├── init_processing_step.m │ │ ├── load.m │ │ ├── matlabbatch │ │ │ ├── mb_specify_and_estimate_1st_level.m │ │ │ └── mb_specify_and_estimate_1st_level_Bayesian.m │ │ ├── plot.m │ │ ├── plot_stat_images.m │ │ ├── realign.m │ │ ├── redo.m │ │ ├── restore.m │ │ ├── save.m │ │ ├── set_save_path.m │ │ ├── smooth.m │ │ ├── specify_and_estimate_1st_level.m │ │ ├── t_filter.m │ │ └── undo.m │ └── @MrUnitTest │ │ ├── MrAffineGeometry_affineMatrix.m │ │ ├── MrAffineGeometry_constructor.m │ │ ├── MrAffineGeometry_load_from_file.m │ │ ├── MrAffineGeometry_transformation.m │ │ ├── MrDataNd_arithmetic_operation.m │ │ ├── MrDataNd_constructor.m │ │ ├── MrDimInfo_constructor.m │ │ ├── MrDimInfo_get_add_remove.m │ │ ├── MrDimInfo_index2sample.m │ │ ├── MrDimInfo_load_from_file.m │ │ ├── MrDimInfo_permute.m │ │ ├── MrDimInfo_select.m │ │ ├── MrDimInfo_split.m │ │ ├── MrImageGeometry_constructor.m │ │ ├── MrImageGeometry_create_empty_image.m │ │ ├── MrImageGeometry_load_from_file.m │ │ ├── MrUnitTest.m │ │ ├── affineGeom-fmri.mat │ │ ├── affineGeom-fmri_short.mat │ │ ├── affineGeom-meanfmri.mat │ │ ├── affineGeom.mat │ │ ├── dimInfo-fmri.mat │ │ ├── dimInfo-fmri1.mat │ │ ├── dimInfo-fmri_short.mat │ │ ├── dimInfo-meanfmri.mat │ │ ├── dimInfo-split.mat │ │ ├── dimInfo.mat │ │ ├── imageGeom-fmri.mat │ │ ├── imageGeom-fmri_short.mat │ │ ├── imageGeom-meanfmri.mat │ │ ├── imageGeom-split.mat │ │ ├── imageGeom.mat │ │ ├── make_MrImageGeometry_reference.m │ │ ├── make_affineGeometry_reference.m │ │ ├── make_dimInfo_reference.m │ │ └── make_imageGeometry_reference.m ├── enumerations │ └── CoordinateSystems.m └── utils │ ├── bundle_struct.m │ ├── compatibility │ ├── flip_compatible.m │ ├── spm_create_vol.m │ ├── spm_write_vol.m │ ├── uniqc_spm_imatrix.m │ └── uniqc_spm_matrix.m │ ├── copy_with_hdr.m │ ├── delete_with_hdr.m │ ├── filter_propval.m │ ├── find_processing_folder.m │ ├── find_string.m │ ├── folder2image.m │ ├── get_common_prefix.m │ ├── get_data_type_from_n_voxels.m │ ├── get_dim_labels_from_string.m │ ├── get_filenames.m │ ├── get_path.m │ ├── get_vol_filenames.m │ ├── move_with_hdr.m │ ├── new_class.m │ ├── new_enum.m │ ├── new_function.m │ ├── new_method.m │ ├── new_script.m │ ├── notesUnitTest.m │ ├── plot │ ├── add_colorbars.m │ ├── add_overlay.m │ ├── get_brightened_color.m │ ├── get_fig_name.m │ ├── hline.m │ ├── isNewGraphics.m │ ├── labeled_montage.m │ ├── save_fig.m │ ├── str2fn.m │ ├── str2label.m │ ├── view3d.m │ └── vline.m │ ├── prefix_files.m │ ├── propval.m │ ├── read_cpx_gyrotools │ ├── create_offset_table.m │ ├── create_read_param_struct.m │ ├── read_cpx.m │ ├── read_cpx_header.m │ └── read_cpx_image.m │ ├── read_par_header.m │ ├── recon2image.m │ ├── resizeNd.m │ ├── selection │ ├── convert_selection_array_to_range.m │ └── convert_selection_range_to_array.m │ ├── simplify_path.m │ ├── slider4d │ ├── example_slider4d.m │ ├── plot_abs_image.m │ ├── plot_image_diagnostics.m │ ├── slider4d.fig │ └── slider4d.m │ ├── split_propval.m │ ├── spm_create_vol_with_tr.m │ ├── spm_write_vol_with_tr.m │ ├── strip_fields.m │ ├── test_images │ ├── create_image_with_index_imprint.m │ └── create_shepp_logan_4d.m │ ├── transform_matrix_analyze2matlab.m │ └── transform_matrix_matlab2analyze.m ├── demo ├── MrAffineGeometry │ └── demo_affine_geometry.m ├── MrCopyData │ └── demo_copy_data.m ├── MrDataNd │ └── demo_save.m ├── MrDimInfo │ └── demo_dim_info.m ├── MrImage │ ├── demo_add_overlay.m │ ├── demo_constructor.m │ ├── demo_coregister.m │ ├── demo_image_math_imcalc_fslmaths.m │ ├── demo_multi_echo_realign.m │ ├── demo_plot_images.m │ ├── demo_roi_analysis.m │ ├── demo_spikes.m │ └── demo_split_complex.m ├── MrImageGeometry │ └── demo_image_geometry.m └── MrSeries │ ├── demo_fmri_qa.m │ ├── demo_model_estimation_1st_level.m │ ├── demo_model_estimation_1st_level_Bayesian.m │ ├── 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