├── .gitignore ├── .gitmodules ├── 4d_framework.png ├── 4dflow ├── fcmr_4dflow_drift_correction.m ├── fcmr_4dflow_get_first_moments.m ├── fcmr_4dflow_postprocessing.m ├── fcmr_4dflow_preprocessing.m └── recon_vel_vol.bash ├── 4dflow_volume.gif ├── 4drecon ├── preproc.m ├── recon_cine_vol.bash ├── recon_dc_vol.bash ├── recon_ref_vol.bash └── recon_slice_cine.bash ├── LICENSE ├── README.md ├── cardsync ├── calc_cardiac_timing.m ├── calc_freq.m ├── cardsync_interslice.m ├── cardsync_intraslice.m ├── estimate_heartrate_xf.m ├── fouriershift.m └── nonlconfn.m ├── eval ├── calc_frechet_mean.m ├── plot_info.m ├── read_info_tsv.m ├── summarise_recon.m └── summarise_transformations.m ├── lib ├── 4dflow │ ├── get_cine_vol_force_exclude.m │ ├── get_goalc_parameters.m │ ├── get_pcmr_orientation_parameters.m │ ├── gradfirstmom_mps2world.m │ ├── phase_correction_poly.m │ └── vmps2vworld.m ├── PolyfitnTools │ ├── polydern.m │ ├── polyfitn.m │ ├── polyn2sym.m │ ├── polyn2sympoly.m │ └── polyvaln.m ├── general_tools │ ├── freeROI.m │ ├── implay_RR.m │ ├── imtar.m │ ├── ind2subV.m │ ├── montage_RR.m │ ├── roi2sig.m │ ├── rot_ms.m │ └── vtkwrite.m └── nifti │ ├── FAQ.pdf │ ├── NIfTI_tools.pdf │ ├── UseANALYZE.pdf │ ├── affine.m │ ├── bipolar.m │ ├── bresenham_line3d.m │ ├── clip_nii.m │ ├── collapse_nii_scan.m │ ├── examples.txt │ ├── expand_nii_scan.m │ ├── extra_nii_hdr.m │ ├── flip_lr.m │ ├── get_nii_frame.m │ ├── license.txt │ ├── load_nii.m │ ├── load_nii_ext.m │ ├── load_nii_hdr.m │ ├── load_nii_img.m │ ├── load_untouch0_nii_hdr.m │ ├── load_untouch_header_only.m │ ├── load_untouch_nii.m │ ├── load_untouch_nii_hdr.m │ ├── load_untouch_nii_img.m │ ├── make_ana.m │ ├── make_nii.m │ ├── mat_into_hdr.m │ ├── pad_nii.m │ ├── reslice_nii.m │ ├── rri_file_menu.m │ ├── rri_orient.m │ ├── rri_orient_ui.m │ ├── rri_select_file.m │ ├── rri_xhair.m │ ├── rri_zoom_menu.m │ ├── save_nii.m │ ├── save_nii_ext.m │ ├── save_nii_hdr.m │ ├── save_untouch0_nii_hdr.m │ ├── save_untouch_header_only.m │ 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