Public Types | Public Member Functions

Tractography Class Reference

This class performs the tractography and saves each step. More...

#include <tractography.h>

List of all members.

Public Types

enum  model_type {
  _1T, _1T_FW, _1T_FULL, _1T_FW_FULL,
  _2T, _2T_FW, _2T_FULL, _2T_FW_FULL,
  _3T, _3T_FULL
}

Public Member Functions

 Tractography (FilterModel *model, model_type filter_model_type, const std::string &output_file, const std::string &output_file_with_second_tensor, const bool record_fa, const bool record_nmse, const bool record_trace, const bool record_state, const bool record_cov, const bool record_free_water, const bool record_tensors, const bool transform_position, const bool store_glyphs, const bool branchesOnly, const double fa_min, const double ga_min, const double seedFALimit, const int num_tensors, const int seeds_per_voxel, const double minBranchingAngle, const double maxBranchingAngle, const bool is_full_model, const bool free_water, const double stepLength, const double maxHalfFiberLength, const std::vector< int > &labels, double p0, double sigma_signal, double sigma_mask, double min_radius, double full_brain_ga_min, const int num_threads)
 ~Tractography ()
bool LoadFiles (const std::string &data_file, const std::string &seed_file, const std::string &mask_file, const bool normalized_DWI_data, const bool output_normalized_DWI_data)
void Init (std::vector< SeedPointInfo > &seed_infos)
void Run ()
void Follow3T (const int thread_id, const size_t seed_index, const SeedPointInfo &seed, Fiber &fiber, bool is_branching, std::vector< SeedPointInfo > &branching_seeds, std::vector< BranchingSeedAffiliation > &branching_seed_affiliation)
void Follow2T (const int thread_id, const size_t seed_index, const SeedPointInfo &seed, Fiber &fiber, bool is_branching, std::vector< SeedPointInfo > &branching_seeds, std::vector< BranchingSeedAffiliation > &branching_seed_affiliation)
void Follow1T (const int thread_id, const SeedPointInfo &seed, Fiber &fiber)

Detailed Description

This class performs the tractography and saves each step.


Member Enumeration Documentation

Defines a type to specify the model


Constructor & Destructor Documentation

Tractography::Tractography ( FilterModel model,
model_type  filter_model_type,
const std::string &  output_file,
const std::string &  output_file_with_second_tensor,
const bool  record_fa,
const bool  record_nmse,
const bool  record_trace,
const bool  record_state,
const bool  record_cov,
const bool  record_free_water,
const bool  record_tensors,
const bool  transform_position,
const bool  store_glyphs,
const bool  branchesOnly,
const double  fa_min,
const double  ga_min,
const double  seedFALimit,
const int  num_tensors,
const int  seeds_per_voxel,
const double  minBranchingAngle,
const double  maxBranchingAngle,
const bool  is_full_model,
const bool  free_water,
const double  stepLength,
const double  maxHalfFiberLength,
const std::vector< int > &  labels,
double  p0,
double  sigma_signal,
double  sigma_mask,
double  min_radius,
double  full_brain_ga_min,
const int  num_threads 
)

Constructor, is called from main.cc where all parameters are defined.

Tractography::~Tractography (  ) 

Destructor


Member Function Documentation

void Tractography::Follow1T ( const int  thread_id,
const SeedPointInfo seed,
Fiber fiber 
)

Follows one seed point for the 1 Tensor case

void Tractography::Follow2T ( const int  thread_id,
const size_t  seed_index,
const SeedPointInfo seed,
Fiber fiber,
bool  is_branching,
std::vector< SeedPointInfo > &  branching_seeds,
std::vector< BranchingSeedAffiliation > &  branching_seed_affiliation 
)

Follows one seed point for the 2 Tensor case

void Tractography::Follow3T ( const int  thread_id,
const size_t  seed_index,
const SeedPointInfo seed,
Fiber fiber,
bool  is_branching,
std::vector< SeedPointInfo > &  branching_seeds,
std::vector< BranchingSeedAffiliation > &  branching_seed_affiliation 
)

Follows one seed point for the 3 Tensor case

void Tractography::Init ( std::vector< SeedPointInfo > &  seed_infos  ) 

Creates the seeds and initilizes them by finding the tensor directions, eigenvalues and Euler Angles. This also sets the initial state and covariance.

bool Tractography::LoadFiles ( const std::string &  data_file,
const std::string &  seed_file,
const std::string &  mask_file,
const bool  normalized_DWI_data,
const bool  output_normalized_DWI_data 
)

Load the files that contain the DWI signal, the seeds and a mask defining the volume of the brain.

void Tractography::Run (  ) 

Performs the tractography


The documentation for this class was generated from the following files:
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