Centerline Tool

**Version: 2.0 **Release Date: **Languages: - Matlab - SQL (optional) **Dependencies: - Matlab R2020B or newer - Image Processing Toolbox - **Contributors: - Aaron Ward

Quickstart

1. Type centerline_tool in Matlab command window
2. Load VIPR data via Load Data
3. Perform background phase correction
4. Perform feature extraction via Feature Extraction
5. Select vessels via Select Vessel and Segment
6. View segmented vessels and corresponding vessel parameter plots
7. Save necessary data via Save Data

Synopsis

Centerline Tool is a Matlab-based GUI to analyze phase contrast vastly-undersampled projection reconstruction (PC VIPR) MRI data, specifically of the brain. Depending on the velocity encoding (VENC) used during the MRI acquisition, various cerebral vessels will be available for analysis.

Prerequisites

Please see "Dependencies" for necessary software. Hardware: - Processor: - RAM: Minimum 8 GB - Video card:
Each PC VIPR scan data must already be reconstructed into the desired number of frames and each scan stored in its own directory. Centerline Tool does not perform the necessary reconstruction.

centerline_tool.mlapp

Matlab app designer application Main GUI for loading data, performing preprocessing, and calling most other GUIs

Properties public - vipr_obj: - main object for containing all of the necessary data related to the analysis. - Created by the loadVIPR class. private - phase_correction_app: - property to contain the background_phase_correction_app.mlapp object. - vessel_3D_app: - property to contain the Vessel3D_gui.mlapp object. - vasculature_patch: - image patch object for displaying vasculature

Functions public - viewAngio(app): 1. view 3D vasculature after background phase correction - end_vessel_selection(app, vessel_struct): 1. calculate selected vessel parameters 2. place in structure 3. call Vessel3D_gui.mlapp

Callbacks - startupFcn(app) - runs at app creation. 1. centers window.

- `LoadDataButtonPushed(app, event)`
    - callback for "Load Data" button. 
    1. deletes any instantiated *vipr_obj*
    2. calls `loadVIPR` class to create new instance of *vipr_obj*.
    3. calls `BackgroundPhaseCorrectionButtonPushed` callback.
    
- `DBConnectionButtonPushed(app, event)`
    *currently not programmed*
    - callback for "DB Connection" button.
    1. establish connection with MS SQL server and database.
    
- `ReorientButtonPushed(app, event)`
    - callback for "Reorient" button.
    1. reorients 3D vasculature in radiological coronal view
    
- `BackgroundPhaseCorrectionButtonPushed(app, event)`
    - callback for "Background Phase Correction" button.
    1. calls `background_phase_correction_gui.mlapp` to perform background phase correction
        - object is stored in *app.phase_correction_app* property
    
- `DrawROIButtonPushed(app, event)`
    *current not programmed*
    - callback for "Draw ROI" button.
    1. draw ROI
    
- `ViewParametricMapButtonPushed(app, event)`
    *currently not programmed*
    - callback for "View Parametric Map" button.
    
- `FeatureExtractionButtonPushed(app, event)`
    - callback for "Feature Extraction" button
    1. calls `feature_extraction.m`
        - outputs stored in *app.branchMat* and *app.branchList*

- `SelectVesselandSegmentButtonPushed(app, event)`
    -callback for "Select Vessel and Segment" button
    1. calls `SelectVessel` class to perform vessel selection and subsequent segmentation and visualization
        - object not stored in app property
        
- `UIFigureCloseRequest(app, event)`
    - callback for window closing
    1. delete any children windows
    2. delete self

background_phase_correction_gui.mlapp

Matlab app designer application GUI for performing background phase correction

Properties private - image - default = 0.5 - vmax - default = 0.1 - cd_thresh - default = 0.15 - noise_thresh - default = 0.15 - fit_order - default = 2 - apply_correction - default = 1 - img1_obj - img2_obj - centerline_tool_obj - phase_correction_obj

Functions private - init_backgroundPhaseCorrection(app) - updateImages(app) - saveVariables(app) - image_value_callback(app)

Callbacks - startupFcn - image_sliderValueChanged(app, event) - image_spinnerValueChanged(app, event) - vmax_sliderValueChanged(app, event) - vmax_spinnerValueChanged(app, event) - cd_sliderValueChanged(app, event) - cd_spinnerValueChanged(app, event) - noise_sliderValueChanged(app, event) - noise_spinnerValueChanged(app, event) - reset_fit_buttonButtonPushed(app, event) - update_buttonButtonPushed(app, event) - done_buttonButtonPushed(app, event) - UIFigureCloseRequest(app, event)

Vessel3D_gui.mlapp

Matlab app designer application GUI for visualization of selected vessels

Properties public - centerline_app - current_vessel

*private*
    - `parameter_plot_app`
    - `full_vasculature_patch`
    - `vessel_patch`
    - `ITPlane`
    - `plane`
    - `tb`

Functions public - add_plane(app) - update_spinners(app, value)

*private*
    - `init_axes(app)`
    - `init_window(app)`
    - `plot_full_vasculature(app)`
    - `plot_vessel(app)`
    - `add_voxel_labels(app)`

Callbacks - startupFcn(app, centerline_app) - WindowSpinnerValueChanged(app, event) - LowerVoxelSpinnerValueChanged(app, event) - IsolateVesselSegmentSwitchValueChanged(app, event) - ReorientButtonPushed(app, event) - VesselDropDownValueChanged(app, event) - vessel3DCloseRequest(app, event)

parameter_plot_gui.mlapp

Matlab app designer application GUI for visualization of selected vessel parameter plots (e.g. area, flow, etc.) and saving of data

Properties

Functions

Callbacks

loadVIPR

class creates main vipr_obj that will contain all necessary data regarding the current data set being analyzed

Properties public - directory - source directory of data - fov - field of view - MAG - MAG data - nframes - number of reconstructed frames - res - spatial (?) resolution - time_res - time resolution - velocity - velocity array - vMean - mean velocity array - venc - velocity encoding

Methods private - getDirectory(self) - open folder selection UI to select desired folder - read_header(self) - read vipr header file - returns data_array cell array - parseArray(self, data_array) - parse data_array and set select properties - loadVelocity(self) - load velocity data within .dat files - loadMAG(self) - load MAG data - loadvMean(self) - load mean velocity data - loadDat(self, fname) - read .dat file, reshape array, and cast as single data type - delete(self) - delete object if error is encountered

backgroundPhaseCorrection

calculateParameters

dbSave

MAGrgb

saveData

SelectVessel

feature_extraction

centerline

thinning

FillEulerLUT

p_EulerInv

p_is_simple

p_oct_label

pk_get_nh

pk_get_nh_idx

Skeleton3D

copyUIAxes

makeITPlane