Developer documentation
Version 3.0.3-105-gd3941f44
MR::Filter::DWIBrainMask Class Reference

a filter to compute a whole brain mask from a DWI image. More...

#include "filter/dwi_brain_mask.h"

Inheritance diagram for MR::Filter::DWIBrainMask:
MR::Filter::Base MR::Header

Protected Attributes

const Eigen::MatrixXd & grad
- Protected Attributes inherited from MR::Filter::Base
std::string message
- Protected Attributes inherited from MR::Header
vector< Axis > axes_
transform_type transform_
std::string name_
KeyValues keyval_
const char * format_
std::unique_ptr< ImageIO::Baseio
 additional information relevant for images stored on file More...
DataType datatype_
 the type of the data as stored on file More...
default_type offset_
 the values by which to scale the intensities More...
default_type scale_
std::array< size_t, 3 > realign_perm_
std::array< bool, 3 > realign_flip_

Additional Inherited Members

- Protected Member Functions inherited from MR::Header
void acquire_io (Header &H)
void check (const Header &H) const
void realign_transform ()
 realign transform to match RAS coordinate system as closely as possible More...
void sanitise_voxel_sizes ()
void sanitise_transform ()
void sanitise_strides ()

Detailed Description

a filter to compute a whole brain mask from a DWI image.

Both diffusion weighted and b=0 volumes are required to obtain a mask that includes both brain tissue and CSF.

Typical usage:

auto grad = DWI::get_DW_scheme (input);
Filter::DWIBrainMask dwi_brain_mask_filter (input, grad);
auto output = Image<bool>::create (argument[1], dwi_brain_mask_filter);
dwi_brain_mask_filter (input, output);
const Eigen::MatrixXd & grad
static Image create(const std::string &image_name, const Header &template_header, bool add_to_command_history=true)
Definition: image.h:192
static Image open(const std::string &image_name, bool read_write_if_existing=false)
Definition: image.h:189
vector< ParsedArgument > argument
the list of arguments parsed from the command-line
Eigen::MatrixXd get_DW_scheme(const Header &header, BValueScalingBehaviour bvalue_scaling=BValueScalingBehaviour::Auto)
get the fully-interpreted DW gradient encoding matrix

Definition at line 57 of file dwi_brain_mask.h.

Member Data Documentation

◆ grad

const Eigen::MatrixXd& MR::Filter::DWIBrainMask::grad

Definition at line 150 of file dwi_brain_mask.h.

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