USAGE:
MeshFromDiscreteFiberODF [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--debug] [-p] [--st]
[--nolighting] [--nonormal] [--zoom <double>]
[--png <std::string>] [--bg
<std::vector<double>>] [--angle
<std::vector<double>>] [--size
<std::vector<int>>] [--tau <double>]
[--colorscheme <DIRECTION|MAGNITUDE>]
[--nostretch] [--removenegative] [--basisType
<TENSOR|CYLINDER>] [--basicshape <TETRAHEDRON
|OCTAHEDRON|ICOSAHEDRON>] [--tessorder <int>]
[--scale <double>] [--slice
<std::vector<int>>] [--box <std::vector<int>>]
[--flip <std::vector<int>>] [--pow <double>]
[--iso] [--tensorISO <double>] [--tensor
<std::vector<double>>] [--odfOrder <int>]
[--outputType <DWI|EAP|ODF>] [--radius
<double>] [--normalize <NONE|MIN_MAX|UNIT_MAX
|UNIT_INTEGRAL>] [--orientations
<std::string>] [--mask <std::string>] [-o
<std::string>] [--] [--version] [-h]
<std::string>
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (value: 0)
--xml
Produce xml description of command line arguments (value: 0)
--echo
Echo the command line arguments (value: 0)
--debug
debug (value: 0)
-p, --progress
show progress of processing (value: 0)
--st
Use single thread. (value: 0)
--nolighting
Set LightingOff. (value: 0)
--nonormal
Do not use vtkPolyDataNormals. (value: 0)
--zoom <double>
zoom factor. Used when visualzing the vtk file.
--png <std::string>
output png file. Used when visualzing the vtk file.
--bg <std::vector<double>>
background color for the window (value: 0,0,0)
--angle <std::vector<double>>
azimuth,elevation. Used when visualzing the vtk file. (value: 0.0,0.0)
--size <std::vector<int>>
window size. Used when visualzing the vtk file. (value: 600,600)
--tau <double>
Tau value. The default is calculated based on 4*pi*pi*tau=1. (value:
0.0253303)
--colorscheme <DIRECTION|MAGNITUDE>
Color scheme. (value: DIRECTION)
--nostretch
If it is set, the mesh in each voxel is a sphere and the values of the
spherical function are only for coloring. (value: 0)
--removenegative
Remove negative values if set. (value: 0)
--basisType <TENSOR|CYLINDER>
Type of basis. (value: TENSOR)
--basicshape <TETRAHEDRON|OCTAHEDRON|ICOSAHEDRON>
Basic shape for subdivision. (value: ICOSAHEDRON)
--tessorder <int>
Tessellation order. (value: 4)
--scale <double>
Scale factor. (value: 1)
--slice <std::vector<int>>
coordinates for coronal, sagittal and transverse views. When -1 is
used for x/y/z, then the voxel is visible in the x/y/z-axis. (value:
-1,-1,-1)
--box <std::vector<int>>
only generate mesh from a given box (x0,x1,y0,y1,z0,z1). When -1 is
used, then x0/y0/z0 will be 0, x1/y1/z1 will be the maximal number in
the x/y/z-axis. (value: -1,-1,-1,-1,-1,-1)
--flip <std::vector<int>>
Flip x/y/z-axis for spherical functions. 1 means flip, 0 means
no-flip. (value: 0,0,0)
--pow <double>
Power factor. (value: 1)
--iso
If set, use isotropic component. (value: 0)
--tensorISO <double>
Isotropic component for tensor. If it is negative, do not use
isotropic component. (value: -1)
--tensor <std::vector<double>>
Three eigenvalues for tensor basis. If two are given, then the last
two eigenvalues are the same. (value: 0.0017,0.0002,0.0002)
--odfOrder <int>
Order for the ODF output. (value: 2)
--outputType <DWI|EAP|ODF>
Type of output. (value: DWI)
--radius <double>
Radius for DWI/EAP profile. It is b value if outputType==DWI.
It is r value if outputType==EAP or outputType==ODF. (value: -1)
--normalize <NONE|MIN_MAX|UNIT_MAX|UNIT_INTEGRAL>
Perform normalization after removing negative values (if set); NONE:
No normalization; MIN_MAX: Min-max normalization; UNIT_MAX: Unit
maximum; UNIT_INTEGRATION: Unit integration. (value: NONE)
--orientations <std::string>
text file which contains orientations. If it is not set, the output is
SH coefficients. If set, the output is EAP/DWI samples
--mask <std::string>
Mask file.
-o <std::string>, --output <std::string>
Output vtk file. If it is not set, visualize the vtk file. (value: "")
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
<std::string>
(required) Input file.
Description: Create a mesh (a spherical profile of DWI/EAP/ODF) from
discrete fiber ODF for visualization.
Examples:
MeshFromDiscreteFiberODF dwi_bw.spr -o dwi_odf_vis.vtk --tessorder 4
--basisType TENSOR --tensor 0.0017,0.0002 --scale 1.5 --colorscheme
MAGNITUDE --outputType ODF --tensorISO 0.7e-3 --iso
MeshFromDiscreteFiberODF dwi_bw.spr --tessorder 4 --basisType TENSOR
--tensor 0.0017,0.0002 --scale 1.5 --colorscheme MAGNITUDE --outputType
ODF --tensorISO 0.7e-3 --iso
Author(s): Jian Cheng (jian.cheng.1983@gmail.com)
Acknowledgements: Thank you everyone.
