rpipe 0.1.4 → 0.1.6

data/.gitignore

@@ -0,0 +1,24 @@
+## MAC OS
+.DS_Store
+
+## TEXTMATE
+._*
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+Gemfile.lock
+
+## PROJECT::SPECIFIC
+doc

data/Gemfile

@@ -1,4 +1,6 @@
 source "http://rubygems.org"
 
+# gem 'metamri', :path => '~/code/metamri'
+
 # Specify your gem's dependencies in rpipe.gemspec
 gemspec

data/Rakefile

@@ -1,26 +1,6 @@
 require 'rubygems'
 require 'rake'
-
-begin
-  require 'jeweler'
-  Jeweler::Tasks.new do |gem|
-    gem.name = "rpipe"
-    gem.summary = %Q{Neuroimaging preprocessing the Ruby way}
-    gem.description = %Q{Neuroimaging preprocessing the Ruby way}
-    gem.email = "kjkosmatka@gmail.com"
-    gem.homepage = "http://github.com/brainmap/rpipe"
-    gem.authors = ["Kristopher Kosmatka", "Erik Kastman"]
-    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
-    gem.add_dependency "metamri"
-    gem.add_dependency "log4r"
-    gem.add_dependency "POpen4"
-    gem.add_dependency "ruport"
-    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
-  end
-  Jeweler::GemcutterTasks.new
-rescue LoadError
-  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
-end
+require 'bundler/gem_tasks'
 
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
@@ -66,8 +46,8 @@ begin
 rescue LoadError
   "Not using darkfish."
 end
-require 'rake/rdoctask'
-Rake::RDocTask.new do |rdoc|
+require 'rdoc/task'
+RDoc::Task.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 
   rdoc.rdoc_dir = 'rdoc'

data/bin/create_driver.rb

@@ -31,6 +31,8 @@ def create!
       end
     rescue StandardError => e
       puts "Problem creating driver for #{rawdir}"
+      puts e 
+      puts e.backtrace if cli_options[:verbose]
     end
   end
 end
@@ -81,6 +83,10 @@ def parse_options
     opts.on('-f', '--force', "Overwrite drivers if they exist.") do
       options[:force] = true
     end
+    
+    opts.on('-v', '--verbose', "Print extra info.") do
+      options[:verbose] = true
+    end
 
     opts.on_tail('-h', '--help', "Show this message")  { puts(parser); exit }
     opts.on_tail("Example: #{File.basename(__FILE__)} mrt00001")

data/bin/create_onsets_files.rb

@@ -0,0 +1,74 @@
+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', 'lib')
+require 'rubygems'
+require 'optparse'
+require 'logfile'
+require 'pathname'
+
+def create!
+  # Parse CLI Options and Spec File
+  cli_options = parse_options
+  
+  # Extract Onsets Files from Log Text Files
+  while ARGV.size >= 1
+    begin
+      filename = ARGV.shift
+      basename = File.basename(filename)
+    
+      log = Logfile.new(filename, *cli_options[:conditions])
+      puts log.to_csv
+      log.write_csv(basename + '.csv')
+      log.write_mat(filename)
+    rescue StandardError => e
+      puts "Problem creating onsets for #{filename}"
+      puts e 
+      puts e.backtrace if cli_options[:verbose]
+    end
+  end
+  
+end
+
+
+def parse_options
+  options = { :config => {} }
+  parser = OptionParser.new do |opts|
+    opts.banner = "Usage: #{File.basename(__FILE__)} [options] RAWDIR(S)"
+
+    opts.on('-f', '--files FILES', "Logfiles to Extract onsets from")     do |files| 
+      options[:logfiles] = files.gsub(" ", "").split(',')
+    end
+    
+    opts.on('-c', '--conditions CONDITIONS', "Conditions to extract onsets for") do |conditions_arg|
+      options[:conditions] = conditions_arg.gsub(" ", "").split(",").collect(&:to_sym)
+    end
+    
+    opts.on('-f', '--force', "Overwrite onsets files if they exist.") do
+      options[:force] = true
+    end
+    
+    opts.on('-v', '--verbose', "Print extra info.") do
+      options[:verbose] = true
+    end
+    
+    
+
+    opts.on_tail('-h', '--help', "Show this message")  { puts(parser); exit }
+    opts.on_tail("Example: #{File.basename(__FILE__)} -c 'old, new' pdt00020_bac_081910_faces3_recognitionA.txt pdt00045_lms_112210_faces3_recognitionB.txt")
+  end
+  parser.parse!(ARGV)
+
+  if ARGV.size == 0
+    puts "Problem with arguments - Missing Logfiles to extract!"
+    puts(parser); exit
+  end
+  
+  if options[:conditions].empty?
+    puts "Missing conditions - specify them with -c 'new, old' "
+    puts(parser); exit
+  end
+  
+  return options
+end
+
+# All that for this.
+create!

data/bin/summarize_responses.rb

@@ -37,6 +37,15 @@ def parse_options
   end
   parser.parse!(ARGV)
   
+  unless ARGV.size == 0
+    puts parser, "\n"
+    
+    puts "Sorry, didn't recognize #{ARGV.join(' or ')}"
+    puts "Maybe add -f or -d?", "\n"
+
+    exit
+  end
+  
   return options
 end
 

data/lib/default_methods/default_preproc.rb

@@ -1,3 +1,4 @@
+# Shared preprocessing routines for rpipe 
 module DefaultPreproc
 	
 	# Runs the preprocessing job, including spm job customization, run spm job, and handling motion issues.

data/lib/default_methods/default_recon.rb

@@ -24,7 +24,7 @@ module DefaultRecon
           #   outfile = run_retroicor(scan_spec['physio_files'], outfile)
           # end
 				  
-					slice_time_correct(outfile)
+					slice_time_correct(outfile, scan_spec['alt_direction'] ||= 'alt+z')
 				else
 					File.copy('tmp.nii', outfile)
 				end
@@ -43,6 +43,7 @@ module DefaultRecon
 	def reconstruct_scan(scan_spec, outfile)	
 		if scan_spec['dir']
 		  sequence = DicomRawSequence.new(scan_spec, @rawdir)
+		  File.delete('tmp.nii') if File.exist? 'tmp.nii'
 		  sequence.prepare('tmp.nii')
 			strip_leading_volumes('tmp.nii', outfile, @volume_skip, scan_spec['bold_reps'])
 	  elsif scan_spec['pfile']
@@ -66,9 +67,9 @@ module DefaultRecon
 	end
 	
 	# Uses to3d to slice time correct a 4D functional nifti file.	 Writes result in the current working directory.
-	def slice_time_correct(infile)
+	def slice_time_correct(infile, alt_direction = "alt+z")
 		$Log.info "Slice Timing Correction: #{infile}"
-		cmd = "3dTshift -tzero 0 -tpattern alt+z -prefix a#{infile} #{infile}"
+		cmd = "3dTshift -tzero 0 -tpattern #{alt_direction} -prefix a#{infile} #{infile}"
 		unless run(cmd)
 		  raise ScriptError, "Failed to slice time correct: #{cmd}"
 	  end

data/lib/default_methods/recon/raw_sequence.rb

@@ -55,10 +55,11 @@ module DefaultRecon
     def timing_options(scan_spec, second_file)
       return "" if scan_spec['type'] == "anat"
       instance_offset = scan_spec['z_slices'] + 1
+      alt_direction = scan_spec['alt_direction'] ||= 'alt+z'
       if system("dicom_hdr #{second_file} | grep .*REL.Instance.*#{instance_offset}")
-        return "-epan -time:tz #{scan_spec['bold_reps']} #{scan_spec['z_slices']} 2000 alt+z"
+        return "-epan -time:tz %s %s 2000 %s" % [scan_spec['bold_reps'], scan_spec['z_slices'], alt_direction]
       else
-        return "-epan -time:zt #{scan_spec['z_slices']} #{scan_spec['bold_reps']} 2000 alt+z"
+        return "-epan -time:zt %s %s 2000 %s" % [scan_spec['z_slices'], scan_spec['bold_reps'], alt_direction]
       end
     end
   end

data/lib/logfile.rb

@@ -99,20 +99,31 @@ class Logfile
     File.stat(@textfile).mtime <=> File.stat(other_logfile.textfile).mtime
   end
   
+  # Write a summary table of logfiles to a CSV
+  # Arguments:
+  # * filename : String. Output Filename for CSV
+  # * directory : String. Directory to summarize (defaults to pwd).
+  # * grouping : String. Table attribute to group responses by. (defaults to 'version')
   def self.write_summary(filename = nil, directory = nil, grouping = nil)
     # One usage for this method is from the summarize_responses.rb executible,
     # which doesn't allow for ordered arguments on the fly.  Therefore,
     # assign defaults within the method itself, not the signature.
-    filename ||= 'tmp.csv'
+    filename ||= "logfile_summary.csv"
     directory ||= Dir.pwd
     grouping ||= 'version'
     
     table = self.summarize_directory(directory)
+    
     File.open(filename, 'w') do |f| 
       f.puts Ruport::Data::Grouping(table, :by => grouping).to_csv
     end
   end
-    
+  
+  # Create a Ruport::Data::Table containing summary data for a group of Behavioral logfiles.
+  # Arguments:
+  # * directory : String. Path to a directory to summarize.
+  # 
+  # Raises an IO Error if no logfiles were successfully summarized.
   def self.summarize_directory(directory)
     table = Ruport::Data::Table.new
     Dir.glob(File.join(directory, '*.txt')).each do |logfile| 
@@ -121,6 +132,10 @@ class Logfile
       table << lf.ruport_summary
       table.column_names = lf.summary_attributes if table.column_names.empty?
     end
+    
+    # Ensure that at least some logfiles were found and summarized.
+    raise IOError, "Couldn't find any logfiles in #{directory}" unless table.length >= 1
+    
     return table
   end
   

data/lib/rpipe/version.rb

@@ -0,0 +1,3 @@
+module Rpipe
+  VERSION = "0.1.6"
+end

data/lib/rpipe.rb

@@ -19,6 +19,10 @@ ENV['FSLOUTPUTTYPE'] = 'NIFTI'
 require 'default_logger'
 require 'global_additions'
 
+# Initial Definition of Rpipe Module for Bundler-style gemspec management.
+# TODO: Namespace this gem!
+module Rpipe; end
+
 class JobStep
 	
 	COLLISION_POLICY = :panic # options -- :panic, :destroy, :overwrite

data/rpipe.gemspec

@@ -1,188 +1,27 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "rpipe/version"
 
 Gem::Specification.new do |s|
   s.name = %q{rpipe}
-  s.version = "0.1.4"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.version = Rpipe::VERSION
+  
+  s.summary = %Q{Neuroimaging preprocessing the Ruby way}
+  s.description = %Q{Functional MRI Processing Pipeline for the WADRC}
   s.authors = ["Kristopher Kosmatka", "Erik Kastman"]
-  s.date = %q{2011-03-31}
-  s.description = %q{Neuroimaging preprocessing the Ruby way}
-  s.email = %q{kjkosmatka@gmail.com}
-  s.executables = ["swallow_batch_run.rb", "rpipe", "summarize_responses.rb", "create_driver.rb"]
-  s.extra_rdoc_files = [
-    "LICENSE",
-    "README",
-    "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-    "Gemfile",
-    "LICENSE",
-    "README",
-    "README.rdoc",
-    "Rakefile",
-    "VERSION",
-    "bin/create_driver.rb",
-    "bin/rpipe",
-    "bin/summarize_responses.rb",
-    "bin/swallow_batch_run.rb",
-    "lib/core_additions.rb",
-    "lib/custom_methods/JohnsonMerit220Visit1Preproc.m",
-    "lib/custom_methods/JohnsonMerit220Visit1Preproc.rb",
-    "lib/custom_methods/JohnsonMerit220Visit1Preproc_job.m",
-    "lib/custom_methods/JohnsonMerit220Visit1Stats.m",
-    "lib/custom_methods/JohnsonMerit220Visit1Stats.rb",
-    "lib/custom_methods/JohnsonMerit220Visit1Stats_job.m",
-    "lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m",
-    "lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb",
-    "lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m",
-    "lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m",
-    "lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb",
-    "lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m",
-    "lib/custom_methods/ReconWithHello.rb",
-    "lib/default_logger.rb",
-    "lib/default_methods/default_preproc.rb",
-    "lib/default_methods/default_recon.rb",
-    "lib/default_methods/default_stats.rb",
-    "lib/default_methods/recon/physionoise_helper.rb",
-    "lib/default_methods/recon/raw_sequence.rb",
-    "lib/generators/job_generator.rb",
-    "lib/generators/preproc_job_generator.rb",
-    "lib/generators/recon_job_generator.rb",
-    "lib/generators/stats_job_generator.rb",
-    "lib/generators/workflow_generator.rb",
-    "lib/global_additions.rb",
-    "lib/logfile.rb",
-    "lib/matlab_helpers/CreateFunctionalVolumeStruct.m",
-    "lib/matlab_helpers/import_csv.m",
-    "lib/matlab_helpers/matlab_queue.rb",
-    "lib/matlab_helpers/prepare_onsets.m",
-    "lib/rpipe.rb",
-    "rpipe.gemspec",
-    "spec/generators/preproc_job_generator_spec.rb",
-    "spec/generators/recon_job_generator_spec.rb",
-    "spec/generators/stats_job_generator_spec.rb",
-    "spec/generators/workflow_generator_spec.rb",
-    "spec/helper_spec.rb",
-    "spec/integration/johnson.merit220.visit1_spec.rb",
-    "spec/integration/johnson.tbi.longitudinal.snod_spec.rb",
-    "spec/logfile_spec.rb",
-    "spec/matlab_queue_spec.rb",
-    "spec/merit220_stats_spec.rb",
-    "spec/physio_spec.rb",
-    "test/drivers/merit220_workflow_sample.yml",
-    "test/drivers/mrt00000.yml",
-    "test/drivers/mrt00015.yml",
-    "test/drivers/mrt00015_hello.yml",
-    "test/drivers/mrt00015_withphys.yml",
-    "test/drivers/tbi000.yml",
-    "test/drivers/tbi000_separatevisits.yml",
-    "test/drivers/tmp.yml",
-    "test/fixtures/faces3_recognitionA.mat",
-    "test/fixtures/faces3_recognitionA.txt",
-    "test/fixtures/faces3_recognitionA_equal.csv",
-    "test/fixtures/faces3_recognitionA_unequal.csv",
-    "test/fixtures/faces3_recognitionB_incmisses.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt",
-    "test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt",
-    "test/fixtures/ruport_summary.yml",
-    "test/fixtures/valid_scans.yaml",
-    "test/helper.rb",
-    "test/test_dynamic_method_inclusion.rb",
-    "test/test_includes.rb",
-    "test/test_integrative_johnson.merit220.visit1.rb",
-    "test/test_preproc.rb",
-    "test/test_recon.rb",
-    "test/test_rpipe.rb",
-    "vendor/output_catcher.rb",
-    "vendor/trollop.rb"
-  ]
-  s.homepage = %q{http://github.com/brainmap/rpipe}
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.4.2}
-  s.summary = %q{Neuroimaging preprocessing the Ruby way}
-  s.test_files = [
-    "spec/generators/preproc_job_generator_spec.rb",
-    "spec/generators/recon_job_generator_spec.rb",
-    "spec/generators/stats_job_generator_spec.rb",
-    "spec/generators/workflow_generator_spec.rb",
-    "spec/helper_spec.rb",
-    "spec/integration/johnson.merit220.visit1_spec.rb",
-    "spec/integration/johnson.tbi.longitudinal.snod_spec.rb",
-    "spec/logfile_spec.rb",
-    "spec/matlab_queue_spec.rb",
-    "spec/merit220_stats_spec.rb",
-    "spec/physio_spec.rb",
-    "test/helper.rb",
-    "test/test_dynamic_method_inclusion.rb",
-    "test/test_includes.rb",
-    "test/test_integrative_johnson.merit220.visit1.rb",
-    "test/test_preproc.rb",
-    "test/test_recon.rb",
-    "test/test_rpipe.rb"
-  ]
+  s.email = "ekk@medicine.wisc.edu"
+  s.homepage = "http://github.com/brainmap/rpipe"
 
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
-
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<rpipe>, [">= 0"])
-      s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-      s.add_runtime_dependency(%q<metamri>, [">= 0"])
-      s.add_runtime_dependency(%q<log4r>, [">= 0"])
-      s.add_runtime_dependency(%q<POpen4>, [">= 0"])
-      s.add_runtime_dependency(%q<ruport>, [">= 0"])
-    else
-      s.add_dependency(%q<rpipe>, [">= 0"])
-      s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-      s.add_dependency(%q<metamri>, [">= 0"])
-      s.add_dependency(%q<log4r>, [">= 0"])
-      s.add_dependency(%q<POpen4>, [">= 0"])
-      s.add_dependency(%q<ruport>, [">= 0"])
-    end
-  else
-    s.add_dependency(%q<rpipe>, [">= 0"])
-    s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
-    s.add_dependency(%q<metamri>, [">= 0"])
-    s.add_dependency(%q<log4r>, [">= 0"])
-    s.add_dependency(%q<POpen4>, [">= 0"])
-    s.add_dependency(%q<ruport>, [">= 0"])
-  end
+  s.add_development_dependency "thoughtbot-shoulda", ">= 0"
+  s.add_dependency "metamri", '~>0.2.9'
+  s.add_dependency "log4r", '~>1.1.9'
+  s.add_dependency "POpen4", '~>0.1.4'
+  s.add_dependency "ruport", '~>1.6.3'
+  
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.require_paths = ["lib"]
+  
 end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rpipe
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 23
   prerelease: 
   segments: 
   - 0
   - 1
-  - 4
-  version: 0.1.4
+  - 6
+  version: 0.1.6
 platform: ruby
 authors: 
 - Kristopher Kosmatka
@@ -16,14 +16,13 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-31 00:00:00 -05:00
+date: 2011-08-18 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
+  name: thoughtbot-shoulda
   prerelease: false
-  name: rpipe
-  type: :runtime
-  version_requirements: &id001 !ruby/object:Gem::Requirement 
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -32,134 +31,87 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  requirement: *id001
-- !ruby/object:Gem::Dependency 
-  prerelease: false
-  name: shoulda
   type: :development
-  version_requirements: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id002
-- !ruby/object:Gem::Dependency 
-  prerelease: false
-  name: thoughtbot-shoulda
-  type: :development
-  version_requirements: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id003
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
+  name: metamri
   prerelease: false
-  name: thoughtbot-shoulda
-  type: :development
-  version_requirements: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 5
         segments: 
         - 0
-        version: "0"
-  requirement: *id004
+        - 2
+        - 9
+        version: 0.2.9
+  type: :runtime
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
+  name: log4r
   prerelease: false
-  name: thoughtbot-shoulda
-  type: :development
-  version_requirements: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 1
         segments: 
-        - 0
-        version: "0"
-  requirement: *id005
-- !ruby/object:Gem::Dependency 
-  prerelease: false
-  name: metamri
+        - 1
+        - 1
+        - 9
+        version: 1.1.9
   type: :runtime
-  version_requirements: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id006
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
+  name: POpen4
   prerelease: false
-  name: log4r
-  type: :runtime
-  version_requirements: &id007 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 19
         segments: 
         - 0
-        version: "0"
-  requirement: *id007
-- !ruby/object:Gem::Dependency 
-  prerelease: false
-  name: POpen4
+        - 1
+        - 4
+        version: 0.1.4
   type: :runtime
-  version_requirements: &id008 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  requirement: *id008
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
-  prerelease: false
   name: ruport
-  type: :runtime
-  version_requirements: &id009 !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 9
         segments: 
-        - 0
-        version: "0"
-  requirement: *id009
-description: Neuroimaging preprocessing the Ruby way
-email: kjkosmatka@gmail.com
+        - 1
+        - 6
+        - 3
+        version: 1.6.3
+  type: :runtime
+  version_requirements: *id005
+description: Functional MRI Processing Pipeline for the WADRC
+email: ekk@medicine.wisc.edu
 executables: 
-- swallow_batch_run.rb
+- create_driver.rb
+- create_onsets_files.rb
 - rpipe
 - summarize_responses.rb
-- create_driver.rb
+- swallow_batch_run.rb
 extensions: []
 
-extra_rdoc_files: 
-- LICENSE
-- README
-- README.rdoc
+extra_rdoc_files: []
+
 files: 
 - .document
+- .gitignore
 - Gemfile
 - LICENSE
 - README
@@ -167,6 +119,7 @@ files:
 - Rakefile
 - VERSION
 - bin/create_driver.rb
+- bin/create_onsets_files.rb
 - bin/rpipe
 - bin/summarize_responses.rb
 - bin/swallow_batch_run.rb
@@ -202,6 +155,7 @@ files:
 - lib/matlab_helpers/matlab_queue.rb
 - lib/matlab_helpers/prepare_onsets.m
 - lib/rpipe.rb
+- lib/rpipe/version.rb
 - rpipe.gemspec
 - spec/generators/preproc_job_generator_spec.rb
 - spec/generators/recon_job_generator_spec.rb
@@ -309,6 +263,46 @@ test_files:
 - spec/matlab_queue_spec.rb
 - spec/merit220_stats_spec.rb
 - spec/physio_spec.rb
+- test/drivers/merit220_workflow_sample.yml
+- test/drivers/mrt00000.yml
+- test/drivers/mrt00015.yml
+- test/drivers/mrt00015_hello.yml
+- test/drivers/mrt00015_withphys.yml
+- test/drivers/tbi000.yml
+- test/drivers/tbi000_separatevisits.yml
+- test/drivers/tmp.yml
+- test/fixtures/faces3_recognitionA.mat
+- test/fixtures/faces3_recognitionA.txt
+- test/fixtures/faces3_recognitionA_equal.csv
+- test/fixtures/faces3_recognitionA_unequal.csv
+- test/fixtures/faces3_recognitionB_incmisses.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt
+- test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt
+- test/fixtures/ruport_summary.yml
+- test/fixtures/valid_scans.yaml
 - test/helper.rb
 - test/test_dynamic_method_inclusion.rb
 - test/test_includes.rb