wadrc-bcp-scripts 0.0.6

data/.gitignore

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+doc
+.DS_Store
+._*
+*~
+*.gem
+*.gemspec
+Gemfile.lock

data/.svn/entries

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+8
+
+dir
+146
+file:///Data/vtrak1/SysAdmin/lab_repository/trunk/ImageProcessing/test
+file:///Data/vtrak1/SysAdmin/lab_repository
+
+
+
+2009-05-08T17:32:47.685248Z
+146
+erik
+
+
+svn:special svn:externals svn:needs-lock
+
+
+
+
+
+
+
+
+
+
+
+fd7843e3-2c87-496d-a67a-9fe0c7cb9cb9
+
+reconstruct_dti_test.rb
+file
+
+
+
+
+2009-05-08T17:33:51.000000Z
+692bb730b8001354d2fde46acd336087
+2009-05-08T17:32:47.685248Z
+146
+erik
+has-props
+

data/.svn/format

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+8

data/.svn/prop-base/reconstruct_dti_test.rb.svn-base

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+K 14
+svn:executable
+V 0
+
+END

data/.svn/text-base/reconstruct_dti_test.rb.svn-base

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+#!/bin/env ruby
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'test/unit'
+require 'fileutils'
+require 'dtifit_processing'
+
+class ReconstructDTI_test < Test::Unit::TestCase
+  def setup
+    @input_directory = '/Data/vtrak1/raw/wrap140/wrp002_5938_03072008/017'
+    @output_directory = '/tmp/wrp002/dti'
+    @subject_prefix = 'wrp002'
+  end
+
+  def test_dti_reconstruction_class
+    ReconstructDTI.reconstruct!(@input_directory, @output_directory, @subject_prefix)
+  end
+
+
+  def teardown
+    FileUtils.rm_r @output_directory
+  end
+
+end

data/Gemfile

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+source "http://rubygems.org"
+
+# Specify your gem's dependencies in wadrc-bcp-scripts.gemspec
+gemspec

data/README.md

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+WADRC Basic Common Processing Scripts
+=====================================
+
+These are Basic Common Preprocessing Scripts used at the WADRC Neuroimaging Core
+for basic preprocessing.  

data/Rakefile

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+require 'rubygems'
+require 'rake'
+require 'rake/clean'
+require 'rubygems/package_task'
+require 'rdoc/task'
+require 'rake/testtask'
+require 'bundler/gem_tasks'

data/VERSION

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+0.1.0

data/bin/FS_local_recon

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+#!/usr/bin/env ruby
+# Usage: FS_local_recon <computer> -s <subject> <autorecon_options>
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'optparse'
+require 'etc'
+begin
+  require 'net/ssh'
+rescue LoadError
+  require 'rubygems'
+  require 'net/ssh'
+end
+
+require 'additions/NetSshConnectionSession'
+
+
+def run!(hostname, subject, options = {})
+	local_dir ||= '/Data/FS_local_recon'
+	server_analysis_dir = options[:server_analysis_dir]
+	dataset_path = File.join(server_analysis_dir, subject)
+	fs_home = options[:fs_home] if options[:fs_home]
+
+  ssh_to_host hostname do |ssh|
+    unless fs_home
+      fs_home = case ssh.exec!("uname").chomp
+      when "Darwin" then "/Applications/freesurfer"
+      when "Linux" then "/usr/local/freesurfer"
+      else raise ScriptError, "Can't determine freesurfer home.  Try using --fs-home option if you know what it should be."
+      end
+    end
+    
+    commands = []
+    commands << "mv #{dataset_path} #{local_dir}; chmod -R ug+w #{File.join(local_dir, subject)}"
+    commands << [
+      "export FREESURFER_HOME=#{fs_home}",
+      "source $FREESURFER_HOME/SetUpFreeSurfer.sh",
+  	  "export SUBJECTS_DIR=#{local_dir}",
+  	  "recon-all -s #{subject} #{options[:autorecon_args].join(" ")}"].join(";\n")
+    commands << "mv #{File.join(local_dir, subject)} #{server_analysis_dir}"
+    
+    commands.each { |cmd| puts cmd; ssh.exec_realtime(cmd) }
+  end
+
+end
+
+def ssh_to_host(hostname, &block)
+  Net::SSH.start(hostname, Etc.getlogin) do |ssh|
+    puts "Running commands on: #{hostname}"
+    yield ssh
+  end
+end
+
+def parse_options
+  options = {:server_analysis_dir => '/Data/vtrak1/analyses/freesurfer/subjects', :autorecon_args => ['-autorecon2-cp', '-autorecon3']}
+  parser = OptionParser.new do |opts|
+    opts.banner = "Usage: #{File.basename(__FILE__)} hostname [options]"
+
+    opts.on('-s', '--subject SUBJECT', "Subject to Recon")     do |subject| 
+      options[:subject] = subject
+    end
+    
+    opts.on('-d', '--dir DIR', "Directory if other than default (#{options[:server_analysis_dir]})") do |server_analysis_dir| 
+      options[:server_analysis_dir] = File.expand_path(server_analysis_dir)
+    end
+    
+    opts.on('-r', '--recon-args ARGS', Array, "Arguments list for recon-all") do |args| 
+      options[:autorecon_args] = args
+    end
+    
+    opts.on('-f', '--fs-home DIR', "FREESURFER_HOME directory") do |dir|
+      options[:fs_home] = dir
+    end
+    
+    opts.on_tail('-h', '--help', "Show this message")  { puts(parser); exit }
+    opts.on_tail("Example: #{File.basename(__FILE__)} nelson -s tami99999 --recon-args -autorecon2-cp,-autorecon3")
+  end
+
+  parser.parse!(ARGV)
+  
+  if ARGV.size == 0
+    warn "Error: Missing hostname - maybe you forgot it?"
+    puts(parser); exit
+  end
+  
+  if ARGV.size != 1
+    puts "Problem with arguments: #{ARGV}"
+    puts(parser); exit
+  end
+
+  
+  return options
+end
+
+if File.basename(__FILE__) == File.basename($0)
+  options = parse_options
+  hostname = ARGV.shift
+  run!(hostname, options[:subject], options)
+end

data/bin/FieldmapAtWaisman.rb

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+#!/usr/bin/env ruby
+
+=begin rdoc
+This command-line utility executes local preprocessing required for fieldmapping.  It prepares a tar-file to transfer to a remote machine for processing, in the form:
+
+incoming.tar.gz/
+|-- fieldmap
+|   |-- I0001.dcm
+|   `-- I0002.dcm
+`-- files_to_fieldmap
+    |-- rSnodC.nii
+    `-- rSnodD.nii
+=end
+
+if __FILE__ == $0
+  if ARGV.size != 1
+    puts "Usage: FieldmapAtWaisman.rb "
+  else
+    prefix = ARGV[0]
+    files_to_fieldmap_directory = ARGV[1]
+    dicoms_directory = ARGV[2]
+    
+    
+    t = LocalFieldmapSetup.new(prefix, files_to_fieldmap_directory, dicoms_directory)
+
+    fieldmap_directory = t.find_fieldmap_directory(dicoms_directory)
+    files_to_fieldmap = t.find_files_to_fieldmap(files_to_fieldmap_directory)
+    local_tarfile = t.create_tarfile(prefix, files_to_fieldmap, fieldmap_directory)
+    remote_tarfile = t.transfer_tarfile_to_move(local_tarfile)
+    t.execute_remote_fieldmapping(remote_tarfile)
+    t.transfer_tarfile_from_remote
+    t.unpack_tarfile_locally
+
+  end
+end

data/bin/createFieldmap.rb

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), 'lib')
+
+require 'wadrc-bcp-scripts/FieldmapAtWaisman'
+require 'logger'
+
+=begin rdoc
+This script creates and applies fieldmaps in a scratch directory and handles some basic file zipping and unzipping.
+
+Pass in the path to a tar of fieldmaps and files.  The file should have two directories inside:
+incoming.tar.gz/
+|-- fieldmap
+|   |-- I0001.dcm
+|   `-- I0002.dcm
+`-- files_to_fieldmap
+    |-- rSnodC.nii
+    `-- rSnodD.nii
+=end
+
+if __FILE__ == $0
+  if ARGV.size != 1
+    puts "Usage: createFieldmap.rb incoming_tarfile.tar.gz"
+  else
+    t = FieldmapTask.new(ARGV[0])
+    t.setup_paths
+    tmpdir, fieldmap_directory, files_to_fieldmap = t.unpack(t.incoming_tar_file)
+    Dir.chdir(tmpdir)
+    
+    fieldmap_file = t.create_fieldmap(fieldmap_directory)
+    t.apply_fieldmap(fieldmap_file, files_to_fieldmap)
+    t.cleanup(tmpdir)
+  end
+end

data/bin/preprocess_dti.rb

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+#!/usr/bin/env ruby
+## A command-line DTI-preprocessing script generation utility.
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+require 'yaml'
+require 'optparse'
+begin
+  require 'wadrc-bcp-scripts/basic_task'
+  require 'wadrc-bcp-scripts/dtitask'
+rescue LoadError
+  require 'rubygems'
+  require 'wadrc-bcp-scripts/basic_task'
+  require 'wadrc-bcp-scripts/dtitask'
+end
+
+=begin rdoc
+This library provides basic processing for Diffusion Tensor Images (DTI)
+This command-line processing script takes raw DTI dicoms and outputs FA, MD &
+associated diffusion maps (eigenvalues & eigenvectors).
+
+Currently, the script assumes raw data are unzipped and the output directory
+exists, the glob and DTI params are passed in with a specification file.
+=end
+
+
+def run!
+  # Parse CLI Options and Spec File
+  options = parse_options
+  config = load_spec(options[:spec_file])
+  config.merge!(options)
+  
+  # Create a DTI Preprocessing Flow Task and run it.
+  output_directory = ARGV.pop
+  input_directories = ARGV
+  input_directories.each do |input_directory|
+    task = WadrcBcpScripts::Dtitask.new(config)
+    task.reconstruct!(input_directory, output_directory)
+  end
+end
+
+
+def load_spec(spec_file)
+  if File.exist?(spec_file)
+    YAML::load_file(spec_file)
+  else
+    raise IOError, "Cannot find yaml spec file #{spec_file}"
+  end
+end
+
+
+def parse_options
+  options = {:rotate => true}
+  parser = OptionParser.new do |opts|
+    opts.banner = "Usage: #{File.basename(__FILE__)} [options] input_directory output_directory"
+
+    opts.on('-s', '--spec SPEC', "Spec File for script parameters")     do |spec_file| 
+      options[:spec_file] = spec_file
+    end
+    
+    opts.on('-p', '--prefix PREFIX', "Filename Prefix")     do |prefix| 
+      options[:file_prefix] = prefix
+    end
+
+    opts.on('-d', '--dry-run', "Display Script without executing it.") do
+      options[:dry_run] = true
+    end
+
+    opts.on('-f', '--force', "Overwrite output directory if it exists.") do
+      options[:force_overwrite] = true
+    end
+    
+    opts.on('-m', '--mask MASK', "Add an arbitrary mask to apply to data.") do |mask|
+      options[:mask] = File.expand_path(mask)
+      abort "Cannot find mask #{mask}." unless (File.exist?(options[:mask]) || options[:dry_run])
+    end
+    
+    opts.on('-t', '--tmp', "Sandbox the input directory in the case of zipped dicoms.") do
+      options[:force_sandbox] = true
+    end
+    
+    opts.on('--values VALUES_FILE', "Specify a b-values file.") do |bvalues_file|
+      options[:bvalues_file] = bvalues_file
+    end
+        
+    opts.on('--vectors VECTORS_FILE', "Specify a b-vectors file.") do |bvectors_file|
+      options[:bvectors_file] = bvectors_file
+    end
+    
+    opts.on('--no-rotate', "Don't rotate vectors prior to processing") do
+      options[:rotate] = false
+    end
+    
+
+    opts.on_tail('-h', '--help',          "Show this message")          { puts(parser); exit }
+    opts.on_tail("Example: #{File.basename(__FILE__)} -s configuration/dti_spec.yaml -p pd006 raw/pd006 orig/pd006")
+  end
+  parser.parse!(ARGV)
+
+  if ARGV.size == 0
+    # puts "Problem with arguments: #{ARGV}"
+    puts(parser); exit
+  end
+  
+  return options
+end
+
+
+if File.basename(__FILE__) == File.basename($0)
+  run!
+end

data/bin/run_dti_fit_for_study.sh

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+#!/usr/bin/env bash
+# run_dti_fit_for_study.sh
+# Constructs and runs an interface to the preprocess_dti.rb command line
+# interface for a given study.
+
+
+# Sample Arguments
+# raw_dir=/Data/vtrak1/raw/johnson.predict.visit1
+# study_proc_dir=/Data/vtrak1/preprocessed/visits/johnson.predict.visit1
+# study_prefix=pdt
+# yaml_config=/Data/vtrak1/preprocessed/visits/johnson.predict.visit1/dti_config/dti_config.yaml
+
+raw_dir=$1
+study_proc_dir=$2
+study_prefix=$3
+yaml_config=$4
+
+for directory in ${raw_dir}/${study_prefix}*; do
+	# Assume that directories in /raw are named <subject>_<exam-number>_<date>
+  subject=`basename $directory | awk -F_ '{print $1}'`
+
+	# Full command for running DTI with Eddy Current Correction
+	ruby -rubygems ~erik/code/ImageProcessing/bin/preprocess_dti.rb -t \
+	-s ${yaml_config} -p ${subject} ${raw_dir}/${subject}*/dicoms/*dti* \
+	${study_proc_dir}/${subject}/dti_FSL_recon
+done

data/bin/run_dti_fit_script.sh

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+#!/usr/bin/env bash
+# 05/11/10
+# Full command for running DTI with Eddy Current Correction and Sundry Options
+
+# subject=pdt00001;
+# rawdir=/Data/vtrak1/raw/johnson.predict.visit1
+# procdir=/Data/vtrak1/preprocessed/visits/johnson.predict.visit1/pdt00001/dti_FSL_recon
+# yaml_config=/Data/vtrak1/preprocessed/visits/johnson.predict.visit1/dti_config/dti_config.yaml
+
+
+subject=$1
+rawdir=$2
+procdir=$3
+yaml_config=$4
+
+
+
+
+# This is kinda a shity way of doing it, but...  It's alright.  
+
+# The reason why you have to give it here, at the final call to
+# preprocess_dti.rb, is because it's possible that there are more than one
+# series named dti. The script will handle that, as it will actually process
+# each series that matches /dti/, but only when they're multilple arguments
+# given to the preprocess_dti.rb; other shell scripts (like run_dti_fit_script)
+# would intercept and mess up the arguments.
+
+# We don't need 2 of these shell scripts now.'