wadrc-bcp-scripts 0.0.6

data/spec/examples/johnson.alz.snodrest.visit2.yaml

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+# DTI Processing Configuration File
+# johnson.alz.snodrest.visit2
+# Andy's 3T, 12 Directions
+# Last Edited: 3/24/2010, ekk
+--- 
+:file_glob: "'S*'"
+:volumes: 13
+:slices_per_volume: 39
+:slice_order: altplus
+:bvectors_file: /Data/vtrak1/preprocessed/visits/johnson.alz.snodrest.visit2/DTI_info/preproc_dti/enc12.txt
+:bvalues_file: /Data/vtrak1/preprocessed/visits/johnson.alz.snodrest.visit2/DTI_info/preproc_dti/bvalues
+
+# Optional Defaults
+# :repetition_time: 8000

data/spec/examples/johnson.tbi.aware.visit1.yaml

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+# DTI Processing Configuration File
+# johnson.tbi.aware.visit1
+# Andy's 3T, 12 Directions
+# Last Edited: 3/24/2010, ekk
+--- 
+:file_glob: "'S*'"
+:volumes: 13
+:slices_per_volume: 39
+:slice_order: altplus
+:bvectors_file: /Data/vtrak1/preprocessed/visits/johnson.tbi.aware.visit1/DTI_info/preproc_dti/enc12.txt
+:bvalues_file: /Data/vtrak1/preprocessed/visits/johnson.tbi.aware.visit1/DTI_info/preproc_dti/b-values

data/spec/examples/johnson.wrap140.visit1.yaml

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+# DTI Processing Configuration File
+# johnson.wrap140.visit1
+# UWMR5, 25 Directions
+# Last Edited: 3/24/2010, ekk
+--- 
+:file_glob: "'I*.dcm'"
+:volumes: 26
+:slices_per_volume: 49
+:slice_order: altplus
+:bvectors_file: /Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_Fitting/25_directions_UWhospital_magnet_horizontal_spaces.txt
+:bvalues_file: /Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_Fitting/25_directions_bvalues.txt
+:repetition_time: 12000

data/spec/examples/johnson.wrap140.visit1_TR12s.yaml

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+# DTI Processing Configuration File
+# johnson.wrap140.visit1
+# UWMR5, 25 Directions
+# Last Edited: 3/24/2010, ekk
+--- 
+:file_glob: "'I*.dcm'"
+:volumes: 26
+:slices_per_volume: 49
+:slice_order: altplus
+:bvectors_file: /Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_info/preproc_dti/25_directions_table.txt
+:bvalues_file: /Data/vtrak1/preprocessed/visits/wrap140.visit1/DTI_info/preproc_dti/bvalues
+:repetition_time: 12000

data/spec/examples/spec.yaml

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+# DTI Processing File
+--- 
+:file_glob: "'*.dcm'"
+:volumes: 26
+:slices_per_volume: 48
+:slice_order: altplus
+:bvectors_file: /Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvectors.txt
+:bvalues_file: /Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvalues.txt
+:force_overwrite: true
+:dry_run: false
+:repetition_time: 10000
+
+# Defaults:
+# :file_glob: "'*.0*'"
+# :volumes: 26
+# :slices_per_volume: 49
+# :slice_order: altplus
+# :bvectors_file: /Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_Fitting/25_directions_UWhospital_magnet_horizontal_spaces.csv
+# :bvalues_file: /Data/vtrak1/preprocessed/progs/wrap140.visit1/DTI_Fitting/25_directions_bvalues.txt
+# 
+# Optional: 
+# :repetition_time:

data/spec/factories.rb

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+Factory.define :dtitask do |f|  
+  f.config({
+    :bvectors_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvectors.txt",
+    :bvectors_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvectors.txt", 
+    :bvalues_file=>"/Data/vtrak1/analyses/barb/cathy_temp/25_directions_bvalues.txt", 
+    :file_glob=>"'*.dcm'", 
+    :volumes=>26, 
+    :dry_run=>true, 
+    :slices_per_volume=>48 }
+  )
+end

data/spec/helper_spec.rb

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+require 'rubygems'
+require 'tmpdir'
+require 'pp'
+
+require 'factory_girl'
+require 'factories'
+
+$MRI_DATA = ENV['MRI_DATA'] ||'/Data/vtrak1/raw/test/fixtures/ImageProcessing'

data/test/.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/test/.svn/format

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+8

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

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

data/test/.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/test/reconstruct_dti_test.rb

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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

metadata

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+--- !ruby/object:Gem::Specification 
+name: wadrc-bcp-scripts
+version: !ruby/object:Gem::Version 
+  hash: 19
+  prerelease: 
+  segments: 
+  - 0
+  - 0
+  - 6
+  version: 0.0.6
+platform: ruby
+authors: 
+- Erik Kastman
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-08-30 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: net-ssh
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 2
+        - 2
+        version: "2.2"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: escoffier
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 29
+        segments: 
+        - 0
+        - 1
+        - 3
+        version: 0.1.3
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 9
+        segments: 
+        - 2
+        - 5
+        version: "2.5"
+  type: :development
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: factory_girl
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 5
+        segments: 
+        - 2
+        - 0
+        - 5
+        version: 2.0.5
+  type: :development
+  version_requirements: *id004
+description: This gem contains scripts for basic preprocessing in the Wisconsin Alzheimer's Disease Research Center Neuroimaging Group
+email: ekk@medicine.wisc.edu
+executables: 
+- FS_local_recon
+- FieldmapAtWaisman.rb
+- createFieldmap.rb
+- preprocess_dti.rb
+- run_dti_fit_for_study.sh
+- run_dti_fit_script.sh
+- tensor_transpose.rb
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- .gitignore
+- .svn/entries
+- .svn/format
+- .svn/prop-base/reconstruct_dti_test.rb.svn-base
+- .svn/text-base/reconstruct_dti_test.rb.svn-base
+- Gemfile
+- README.md
+- Rakefile
+- VERSION
+- bin/FS_local_recon
+- bin/FieldmapAtWaisman.rb
+- bin/createFieldmap.rb
+- bin/preprocess_dti.rb
+- bin/run_dti_fit_for_study.sh
+- bin/run_dti_fit_script.sh
+- bin/tensor_transpose.rb
+- lib/.svn/entries
+- lib/.svn/format
+- lib/.svn/prop-base/dti_wrapper.rb.svn-base
+- lib/.svn/prop-base/dtifit_processing.rb.svn-base
+- lib/.svn/text-base/dti_wrapper.rb.svn-base
+- lib/.svn/text-base/dtifit_processing.rb.svn-base
+- lib/additions/NetSshConnectionSession.rb
+- lib/wadrc-bcp-scripts.rb
+- lib/wadrc-bcp-scripts/basic_task.rb
+- lib/wadrc-bcp-scripts/dtitask.rb
+- lib/wadrc-bcp-scripts/fieldmap_classes.rb
+- lib/wadrc-bcp-scripts/freesurfer_roi_task.rb
+- lib/wadrc-bcp-scripts/tensor.rb
+- lib/wadrc-bcp-scripts/version.rb
+- spec/.svn/entries
+- spec/.svn/format
+- spec/FS_local_recon_spec.rb
+- spec/blueprints.rb
+- spec/dtitask_spec.rb
+- spec/examples/johnson.alz.snodrest.visit2.yaml
+- spec/examples/johnson.tbi.aware.visit1.yaml
+- spec/examples/johnson.wrap140.visit1.yaml
+- spec/examples/johnson.wrap140.visit1_TR12s.yaml
+- spec/examples/spec.yaml
+- spec/factories.rb
+- spec/helper_spec.rb
+- test/.svn/entries
+- test/.svn/format
+- test/.svn/prop-base/reconstruct_dti_test.rb.svn-base
+- test/.svn/text-base/reconstruct_dti_test.rb.svn-base
+- test/reconstruct_dti_test.rb
+homepage: http://github.com/brainmap/wadrc-bcp-scripts
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Basic Common Preprocessing Scripts for Neuroimaging Data
+test_files: 
+- spec/FS_local_recon_spec.rb
+- spec/blueprints.rb
+- spec/dtitask_spec.rb
+- spec/examples/johnson.alz.snodrest.visit2.yaml
+- spec/examples/johnson.tbi.aware.visit1.yaml
+- spec/examples/johnson.wrap140.visit1.yaml
+- spec/examples/johnson.wrap140.visit1_TR12s.yaml
+- spec/examples/spec.yaml
+- spec/factories.rb
+- spec/helper_spec.rb
+- test/reconstruct_dti_test.rb