Class: WadrcBcpScripts::Dtitask

Inherits:
BasicTask show all
Defined in:
lib/wadrc-bcp-scripts/dtitask.rb

Overview

This library creates scripts for basic processing for Diffusion Tensor Images (DTI).

The main function reconstruct! takes 3 arguements: A directory of raw DTI dicoms, an output directory and a filename prefix. A set of batch commands using standard imaging tools (AFNI & FSL) are generated and executed to create Fractional Anisotropy (FA), Mean Diffusivity (MD) and associated diffusion maps (eigenvalues & eigenvectors) in the output directory.

The script depends on AFNI to be in the path for reconstruction (to3d) and FSL to be in the path for DTI Data Fitting (eddy_correct, bet & dtifit)

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from BasicTask

#check_setup, #config_requires, #ensure_file_exists, #environment_requires

Constructor Details

#initialize(config = Hash.new) ⇒ Dtitask

Intialize DTItask with the following options:

DTI Options

  • bvectors_file :

  • bvalues_file :

  • repetition_time : TR in milliseconds, defaults to 8000

File Conversion Options

  • file_glob :

  • volumes :

  • slices_per_volume :

  • slice_order:

Runtime Options

  • dry_run :

  • force_overwrite :

  • sandbox : Forces copying and unzipping to a temp directory in the case 

    of zipped dicom files.



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 49

def initialize(config = Hash.new)
  @config = config

  @config[:dry_run] = true if config.empty?

  begin 
    # Intialize Settings for File Conversion and Diffusion Directions and Values
    config_requires :bvectors_file, :bvalues_file, :file_glob, :volumes, 
    :slices_per_volume, :slice_order
  
    # List binaries requried for the script to run.
    environment_requires :to3d, :eddy_correct, :bet, :dtifit, :rotbvecs
  rescue ScriptError => e
    raise e unless @config[:dry_run]
  end

end

Instance Attribute Details

#config ⇒ Object

Task Configuration Options Hash



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 17

def config
  @config
end

#file_prefix ⇒ Object (readonly)

File Prefix to use for processing.



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 25

def file_prefix
  @file_prefix
end

#input_directory ⇒ Object (readonly)

Source Directory of DICOMS



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 19

def input_directory
  @input_directory
end

#output_directory ⇒ Object (readonly)

Destination Directory for DTI vectors, values, and maps



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 23

def output_directory
  @output_directory
end

#working_input_directory ⇒ Object (readonly)

Source Directory of unzipped DICOMS if using a Sandbox (or input_directory if not)



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 21

def working_input_directory
  @working_input_directory
end

Instance Method Details

#construct_commands(input_directory, output_directory, file_prefix) ⇒ Object

Constructs the commands used in the script from constants and variables set during intialization/configuration and gathered by the main reconstruct! function.



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 109

def construct_commands(input_directory, output_directory, file_prefix)
  rep_time = @config[:repetition_time] ? @config[:repetition_time] : 8000
  to3d_recon_options = "-time:zt #{@config[:slices_per_volume]} #{@config[:volumes]} #{rep_time} #{@config[:slice_order]} #{input_directory}/#{@config[:file_glob]}"

  commands = Array.new

  # Recon
  commands << "to3d -prefix #{file_prefix}.nii -session #{output_directory} #{to3d_recon_options}"

  # Eddy Current Correction
  commands << "eddy_correct #{output_directory}/#{file_prefix}.nii #{output_directory}/#{file_prefix}_ecc.nii 0"

  if @config[:rotate]
    # Rotate_bvecs
    subject_bvectors_file = File.join(output_directory, file_prefix + "_" + File.basename(@config[:bvectors_file]))
    commands << "rotbvecs #{@config[:bvectors_file]} #{subject_bvectors_file} #{File.join(output_directory, file_prefix)}_ecc.ecclog"
  else
    subject_bvectors_file = @config[:bvectors_file]
  end


  # Apply Mask
  if @config[:mask]
    out = "#{File.join(output_directory, file_prefix)}_ecc_ss"
    commands << "fslmaths #{@config[:mask]} -mul #{File.join(output_directory, file_prefix)}_ecc #{out}"
  else
    out = "#{File.join(output_directory, file_prefix)}_ecc"
  end
  commands << "bet #{out} #{out}_brain -f 0.1 -g 0 -n -m"

  # Run DTI Fit
  commands << "dtifit --data=#{output_directory}/#{file_prefix}_ecc.nii \
    --out=#{output_directory}/#{file_prefix}_dti \
    --mask=#{out}_brain_mask \
    --bvecs=#{subject_bvectors_file} \
    --bvals=#{@config[:bvalues_file]}"

  return commands
end

#reconstruct!(input_directory, output_directory, file_prefix = nil) ⇒ Object

Reconstruct creates a script of commands to execute in order to prepare DTI data for analyses (take a raw directory of DICOMS, convert them to nifti, eddy current correct them, and fit them using FSL to create eigen vectors and values, and MD and FA maps.

Throws an IOError if input_directory is not found on the filesystem or output directory already exists (except during a dry_run).



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# File 'lib/wadrc-bcp-scripts/dtitask.rb', line 75

def reconstruct!(input_directory, output_directory, file_prefix = nil)
  @input_directory = File.expand_path(input_directory)
  @output_directory = File.expand_path(output_directory)
  @file_prefix = file_prefix ? file_prefix : File.basename(input_directory)

  introduction = "Begin processing #{File.join(@input_directory)}"; puts
  puts "-" * introduction.size
  puts introduction; puts

  begin check_setup unless @config[:dry_run]
  rescue IOError => e
    puts "Error: #{e}"
    exit
  end

  # Construct the Script, output it and run it.
  batch_cmd = construct_commands(@working_input_directory, @output_directory, @file_prefix)

  batch_cmd.each do |cmd|
    puts cmd; $LOG.info cmd
    puts `#{cmd}` unless @config[:dry_run]
    puts
  end

  cleanup unless @config[:dry_run]

  puts "Done processing #{@file_prefix}" unless @config[:dry_run]

end