rpipe 0.0.1

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Files changed (104) hide show
  1. data/.document +5 -0
  2. data/.gitignore +23 -0
  3. data/LICENSE +20 -0
  4. data/README +0 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +78 -0
  7. data/VERSION +1 -0
  8. data/bin/create_driver.rb +79 -0
  9. data/bin/rpipe +131 -0
  10. data/bin/swallow_batch_run.rb +21 -0
  11. data/lib/core_additions.rb +5 -0
  12. data/lib/custom_methods/JohnsonMerit220Visit1Preproc.m +26 -0
  13. data/lib/custom_methods/JohnsonMerit220Visit1Preproc.rb +43 -0
  14. data/lib/custom_methods/JohnsonMerit220Visit1Preproc_job.m +80 -0
  15. data/lib/custom_methods/JohnsonMerit220Visit1Stats.m +74 -0
  16. data/lib/custom_methods/JohnsonMerit220Visit1Stats.rb +63 -0
  17. data/lib/custom_methods/JohnsonMerit220Visit1Stats_job.m +63 -0
  18. data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m +26 -0
  19. data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb +41 -0
  20. data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m +69 -0
  21. data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m +76 -0
  22. data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb +67 -0
  23. data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m +59 -0
  24. data/lib/custom_methods/ReconWithHello.rb +7 -0
  25. data/lib/default_logger.rb +13 -0
  26. data/lib/default_methods/default_preproc.rb +76 -0
  27. data/lib/default_methods/default_recon.rb +80 -0
  28. data/lib/default_methods/default_stats.rb +94 -0
  29. data/lib/default_methods/recon/physionoise_helper.rb +69 -0
  30. data/lib/default_methods/recon/raw_sequence.rb +109 -0
  31. data/lib/generators/job_generator.rb +36 -0
  32. data/lib/generators/preproc_job_generator.rb +31 -0
  33. data/lib/generators/recon_job_generator.rb +76 -0
  34. data/lib/generators/stats_job_generator.rb +70 -0
  35. data/lib/generators/workflow_generator.rb +128 -0
  36. data/lib/global_additions.rb +18 -0
  37. data/lib/logfile.rb +310 -0
  38. data/lib/matlab_helpers/CreateFunctionalVolumeStruct.m +6 -0
  39. data/lib/matlab_helpers/import_csv.m +32 -0
  40. data/lib/matlab_helpers/matlab_queue.rb +37 -0
  41. data/lib/matlab_helpers/prepare_onsets_xls.m +30 -0
  42. data/lib/rpipe.rb +254 -0
  43. data/rpipe.gemspec +177 -0
  44. data/spec/generators/preproc_job_generator_spec.rb +27 -0
  45. data/spec/generators/recon_job_generator_spec.rb +33 -0
  46. data/spec/generators/stats_job_generator_spec.rb +50 -0
  47. data/spec/generators/workflow_generator_spec.rb +97 -0
  48. data/spec/helper_spec.rb +40 -0
  49. data/spec/integration/johnson.merit220.visit1_spec.rb +47 -0
  50. data/spec/integration/johnson.tbi.longitudinal.snod_spec.rb +48 -0
  51. data/spec/logfile_spec.rb +96 -0
  52. data/spec/matlab_queue_spec.rb +40 -0
  53. data/spec/merit220_stats_spec.rb +81 -0
  54. data/spec/physio_spec.rb +98 -0
  55. data/test/drivers/merit220_workflow_sample.yml +15 -0
  56. data/test/drivers/mrt00000.yml +65 -0
  57. data/test/drivers/mrt00015.yml +62 -0
  58. data/test/drivers/mrt00015_hello.yml +41 -0
  59. data/test/drivers/mrt00015_withphys.yml +81 -0
  60. data/test/drivers/tbi000.yml +129 -0
  61. data/test/drivers/tbi000_separatevisits.yml +137 -0
  62. data/test/drivers/tmp.yml +58 -0
  63. data/test/fixtures/faces3_recognitionA.mat +0 -0
  64. data/test/fixtures/faces3_recognitionA.txt +86 -0
  65. data/test/fixtures/faces3_recognitionA_equal.csv +25 -0
  66. data/test/fixtures/faces3_recognitionA_unequal.csv +21 -0
  67. data/test/fixtures/faces3_recognitionB_incmisses.txt +86 -0
  68. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3R_40.txt +13360 -0
  69. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPd3_40.txt +13360 -0
  70. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CPttl_40.txt +13360 -0
  71. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3R_40.txt +13360 -0
  72. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTd3_40.txt +13360 -0
  73. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_CRTttl_40.txt +13360 -0
  74. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3R_40.txt +334 -0
  75. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTd3_40.txt +334 -0
  76. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_CRTttl_40.txt +334 -0
  77. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RRT_40.txt +334 -0
  78. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_RVT_40.txt +334 -0
  79. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_card_spline_40.txt +334 -0
  80. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_HalfTR_resp_spline_40.txt +334 -0
  81. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RRT_40.txt +9106 -0
  82. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_RVT_40.txt +9106 -0
  83. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3R_40.txt +167 -0
  84. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTd3_40.txt +167 -0
  85. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_CRTttl_40.txt +167 -0
  86. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RRT_40.txt +167 -0
  87. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt +167 -0
  88. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_card_spline_40.txt +167 -0
  89. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_resp_spline_40.txt +167 -0
  90. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_card_spline_40.txt +13360 -0
  91. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_40.txt +9106 -0
  92. data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_resp_spline_downsampled_40.txt +9106 -0
  93. data/test/fixtures/ruport_summary.yml +123 -0
  94. data/test/fixtures/valid_scans.yaml +35 -0
  95. data/test/helper.rb +10 -0
  96. data/test/test_dynamic_method_inclusion.rb +10 -0
  97. data/test/test_includes.rb +11 -0
  98. data/test/test_integrative_johnson.merit220.visit1.rb +31 -0
  99. data/test/test_preproc.rb +11 -0
  100. data/test/test_recon.rb +11 -0
  101. data/test/test_rpipe.rb +19 -0
  102. data/vendor/output_catcher.rb +93 -0
  103. data/vendor/trollop.rb +781 -0
  104. metadata +260 -0
data/test/fixtures/physionoise_regressors/EPI__fMRI_Task1_TR_RVT_40.txt ADDED
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