2011 Summer Project Week re-parameterize fiber - Revision history

Cvachet: /* Key Investigators */

2011-06-24T15:22:01Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-22T21:04:48Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-22T21:03:58Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-20T18:52:22Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-20T18:35:33Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-20T17:57:47Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-20T02:25:17Z

Key Investigators

Wendyuu: /* Key Investigators */

2011-06-20T02:24:31Z

Key Investigators

Wendyuu at 02:18, 20 June 2011

2011-06-20T02:18:50Z

Wendyuu at 02:18, 20 June 2011

2011-06-20T02:18:00Z

@@ Line 37: / Line 37: @@
 <!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
 * Bugs are fixed in the tool and GenerateCLP is used to make it a slicer command line module
-* Code is committed to the svn repository on NITRC
+* Code is committed to the svn repository on [http://www.nitrc.org/projects/dti_tract_stat/ NITRC]
 * The tool has the functions now to sample a fiber file (vtk) and generate a profile of FA/MD/AD/RD/l2/l3/GA/FRO along the fibers with different noise model (Gaussian or Beta).  Sampling step size and kernel size used in the noise model could be changed.

@@ Line 36: / Line 36: @@
 <!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
-Bugs are fixed in the tool and GenerateCLP is used to make it a slicer command line module
+* Bugs are fixed in the tool and GenerateCLP is used to make it a slicer command line module
-Code is committed to the svn repository on NITRC
+* Code is committed to the svn repository on NITRC
-The tool has the functions now to sample a fiber file (vtk) and generate a profile of FA/MD/AD/RD/l2/l3/GA/FRO along the fibers with different noise model (Gaussian or Beta).  Sampling step size and kernel size used in the noise model could be changed.
+* The tool has the functions now to sample a fiber file (vtk) and generate a profile of FA/MD/AD/RD/l2/l3/GA/FRO along the fibers with different noise model (Gaussian or Beta).  Sampling step size and kernel size used in the noise model could be changed.
 USAGE:

← Older revision		Revision as of 21:03, 22 June 2011
Line 36:		Line 36:

	<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->		<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
		+	Bugs are fixed in the tool and GenerateCLP is used to make it a slicer command line module
		+	Code is committed to the svn repository on NITRC
		+	The tool has the functions now to sample a fiber file (vtk) and generate a profile of FA/MD/AD/RD/l2/l3/GA/FRO along the fibers with different noise model (Gaussian or Beta). Sampling step size and kernel size used in the noise model could be changed.
		+
		+	USAGE:
		+
		+	dtitractstatCLP [--returnparameterfile <std::string>]
		+	[--processinformationaddress <std::string>] [--xml]
		+	[--echo] [--quantile_percentage <double>] [--stat_type
		+	<mean\|mode\|quantile>] [--noise_model <gaussian\|beta>]
		+	[--parameter_list <std::vector<std::string>>]
		+	[--bandwidth <double>] [--window <int>] [--step_size
		+	<double>] [--image_space] [--window_file <std::string>]
		+	[--plane_file <std::string>] [-o <std::string>] [-i
		+	<std::string>] [--] [--version] [-h]
		+
		+
		+	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.). (default: 0)
		+
		+	--xml
		+	Produce xml description of command line arguments (default: 0)
		+
		+	--echo
		+	Echo the command line arguments (default: 0)
		+
		+	--quantile_percentage <double>
		+	Quantile percentage [0,100] (default value: 50) (default: 50)
		+
		+	--stat_type <mean\|mode\|quantile>
		+	type of maximum likelihood estimate at each point (default: mean)
		+
		+	--noise_model <gaussian\|beta>
		+	noise model used (gaussian or beta) (default: gaussian)
		+
		+	--parameter_list <std::vector<std::string>>
		+	the list of scalar diffusion properties that are calculated. It can be
		+	one or multiple of the following: fa,md,fro,ad,rd,l2,l3,ga (default:
		+	"fa","md","fro","ad","rd","l2","l3","ga")
		+
		+	--bandwidth <double>
		+	bandwidth or standard deviation for the kernel used in modeling noise
		+	(default value: 1 unit) It needs to be larger than 0.1 (default: 1)
		+
		+	--window <int>
		+	window (default value: -1 (no window chosen for visualization)), the
		+	window value lies in range [0,max_number_of_kernel_windows] where
		+	max_number_of_kernel_windows depends on the stepsize chosen and
		+	available arc length range (default: -1)
		+
		+	--step_size <double>
		+	Step size used for sampling the fiber file. It needs to be larger than
		+	0.1 (default: 1)
		+
		+	--image_space
		+	The fiber file is in default in world coordinate space. This argument
		+	changes it to image space (default: 0)
		+
		+	--window_file <std::string>
		+	csv file containing the histogram values for the chosen kernel window
		+
		+	--plane_file <std::string>
		+	File that specifies the plane
		+
		+	-o <std::string>, --ouput_stats_file <std::string>
		+	Ouput statistics file in .fvp format that has the statistics along the
		+	fiber
		+
		+	-i <std::string>, --input_fiber_file <std::string>
		+	input fiber file that needs to be in .vtk format
		+
		+	--, --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.

@@ Line 8: / Line 8: @@
 ==Key Investigators==
-* UNC-Chapel Hill: Yundi Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
+* UNC-Chapel Hill: Yundi(Wendy) Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
 * University of Utah: Anuja Sharma

@@ Line 8: / Line 8: @@
 ==Key Investigators==
-* UNC-Chapel Hill: Yundi Shi, Benjamin Yvernault, Clement Vachet, Martin Styner
+* UNC-Chapel Hill: Yundi Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
 * University of Utah: Anuja Sharma

@@ Line 26: / Line 26: @@
 <!-- What specific things you will be doing during the week: writing code?  trying code on specific datasets?  talking with other attendees?  All of the above? -->
-** Add functionality to the original source code
+* Add functionality to the original source code
-** Make the tool Slicer compatible
+* Make the tool Slicer compatible
+* Use the tool for primate dataset
 </div>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
-Image:Tracts Pval.png
+Image:Tracts Pval.png | P value of changes in diffusion properties visualized along fiber tracts
 </gallery>