Difference between revisions of "2011 Summer Project Week re-parameterize fiber"

From NAMIC Wiki
Jump to: navigation, search
 
(12 intermediate revisions by one other user not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
−
Image:notfound.png|Interesting picture to be added...
+
Image:Tracts Pval.png | P value of changes in diffusion properties visualized along fiber tracts
 
</gallery>
 
</gallery>
  
Line 8: Line 8:
  
 
==Key Investigators==
 
==Key Investigators==
−
* UNC-Chapel Hill: Yundi Shi, Benjamin Yvernault, Martin Styner
+
* UNC-Chapel Hill: Yundi(Wendy) Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
 
* University of Utah: Anuja Sharma
 
* University of Utah: Anuja Sharma
  
Line 17: Line 17:
  
 
<!-- What you plan to achieve during project week goes here -->
 
<!-- What you plan to achieve during project week goes here -->
−
 
+
The dti_tract_stats tool is a command line tool developed to provide statistical information of white matter diffusion properties along fiber tracts, and therefore complements geometric information obtained by tractography with white matter integrity measurements. It calculates statistics on parametrized fiber tract data, represented as sets of streamlines.  The goal of this project week is to add the functionality of 1) re-parametrizing fibers that allows visualizing further generated statistics along the stream lines. 2) Make the tool compatible with Slicer using GenerateCLP
  
 
</div>
 
</div>
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? -->
 
<!-- 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
−
 
+
* Make the tool Slicer compatible
 +
* Use the tool for primate dataset
 
</div>
 
</div>
  
Line 35: 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 [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.
 +
 +
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 53: Line 141:
  
 
#NITRIC distribution
 
#NITRIC distribution
−
#Slicer Module
+
http://www.nitrc.org/projects/dti_tract_stat/
−
##Built-in:
 
−
##Extension -- commandline: 
 
−
##Extension -- loadable:
 

Latest revision as of 15:22, 24 June 2011

Home < 2011 Summer Project Week re-parameterize fiber

  • P value of changes in diffusion properties visualized along fiber tracts

Full Title of Project

Key Investigators

  • UNC-Chapel Hill: Yundi(Wendy) Shi, Clement Vachet, Benjamin Yvernault, Martin Styner
  • University of Utah: Anuja Sharma

Objective

The dti_tract_stats tool is a command line tool developed to provide statistical information of white matter diffusion properties along fiber tracts, and therefore complements geometric information obtained by tractography with white matter integrity measurements. It calculates statistics on parametrized fiber tract data, represented as sets of streamlines. The goal of this project week is to add the functionality of 1) re-parametrizing fibers that allows visualizing further generated statistics along the stream lines. 2) Make the tool compatible with Slicer using GenerateCLP

Approach, Plan

  • Add functionality to the original source code
  • Make the tool Slicer compatible
  • Use the tool for primate dataset

Progress

  • 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.


References

Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

  1. NITRIC distribution

http://www.nitrc.org/projects/dti_tract_stat/

Retrieved from "https://www.na-mic.org/w/index.php?title=2011_Summer_Project_Week_re-parameterize_fiber&oldid=69458"