README.md

3D_Radial_MRI_HEALPix

Repository for preprint and ISBI 2020 abstract.

HEALPix View-order for 3D Radial Self-Navigated Motion-Corrected ZTE MRI https://arxiv.org/abs/1910.10276

IEEE International Symposium on Biomedical Imaging 2020 https://2020.biomedicalimaging.org/

Requires:

1. GNU Octave v5.1.0 https://www.gnu.org/software/octave/

• optim https://octave.sourceforge.io/optim/

2. ImageJ or Fiji https://imagej.nih.gov/ij/ https://imagej.net/Fiji

• Slanted Edge MTF https://imagej.nih.gov/ij/plugins/se-mtf/index.html

To Install:

cd your_src_directory

git clone git:https://github.com/curtcorum/3D_Radial_MRI_HEALPix.git

cd 3D_Radial_MRI_HEALPix

git submodule update --init

To run:

octave

or

octave_gui

octave:1> help generate3DRadialTrajectory4

'generate3DRadialTrajectory4' is a function from the file /home/curt/src/3D_Radial_MRI_HEALPix/generate3DRadialTrajectory4.m

RAWVIEWS = generate3DRadialTrajectory4 (NRES, VARARGIN)

 function rawviews = generate3DRadialTrajectory4( Nres, Nframe, L,
 scheme, comment);

 Nres = 1d resolution parameter...total views will be Nres^2

 Nframe = number of frames in an aquisition grouping, default =
 Nres.

 L = number of segments, default 1 for no grouping) ...ignored

 scheme = 'spiral', 'cubed_sphere', 'mesh_icos', 'fibonacci',
 'hammersley' 'healpix', 'icos_0', or 'oct' from the "spherepts"
 package

 '2d_golden', or 'random' from Magnetic Resonance in Medicine 61:354
 –363 (2009)

 comment = string to be appended to the filename, default is
 timespamp

 saves silent_grad_Nres*.txt file in current dirctory

 rawviews.N_pad is the padding paramter used, rawviews.data is view
 table in array

octave:2> rawviews_test = generate3DRadialTrajectory4( 16, 1, 1, 'spiral', 'test');