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Enhancing Neuroimaging Data Provenance with the LONI Pipeline Workflow

This paper discusses the importance of data provenance in neuroimaging through the use of the LONI Pipeline workflow environment. It emphasizes the necessity of thorough documentation and clarity in tools, processing, and data quality to ensure reproducibility, reusability, and interoperability of neuroimaging data. The work aligns with the challenges and goals outlined in previous studies, focusing on the ease of use across platforms and software versions. Moreover, it illustrates the connections between various processes in neuroimaging analysis.

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Enhancing Neuroimaging Data Provenance with the LONI Pipeline Workflow

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  1. Neuroimaging Data Provenance Using the LONI Pipeline Workflow Environment • Allan MacKenzie-Graham IPAW2008 • Arash Payan • Ivo Dinov • John Van Horn • Arthur W. Toga

  2. Provenance in Neuroimaging • Tools used and data described must be adequately described and documented • Determining data quality • Interpretation • Reproducibility • Reusability • Interoperability 2

  3. First Provenance Challenge (Moreau et. al, 2007) 3

  4. Provenance Systems (Moreau et. al, 2007) 4

  5. Goals of the LONI Provenance System • Description • Data • Processing • Reproducibility • Across platforms • Across compilations • Across software versions • Ease of use 5

  6. Neuroimaging Data Provenance Neuroimaging data provenance Project Subject Species Age Sex Acquisition Scanner Orientation Weighting Field Strength TR TE TI 6

  7. Provenance Editor 7

  8. LONI Pipeline 8

  9. LONI Pipeline Module 9

  10. Workflow Provenance <connections> <connection source="skullstrippedatlas.Output_0" sink="AlignLinear.StandardVolume_0" /> <connection source="SkullStrippedmousedataNORMAL.Output_0" sink="AlignLinear.ResliceVolume_0" /> <connection source="skullstrippedatlasINJECTED.Output_0" sink="AlignLinear.ResliceVolume_0" /> <connection source="AlignLinear.LinearTransformation_0" sink="AffinetoRigid.Full-affineTransformation_0" /> <connection source="AffinetoRigid.Rigid-bodyTransformation_0" sink="Reslice.Input.airLinearTransformation_0" /> <connection source="Reslice.OutputReslicedVolume_0" sink="AnalyzeImagetoMNC.InputAnalyzeImageFile_0" /> <connection source="AnalyzeImagetoMNC.OutputMinc_0" sink="MINCMath.InputMincs_0" /> <connection source="MINCMath.OutputMinc_0" sink="PrintAllLabels.InputMinc_0" /> <connection source="skullstrippedatlas.Output_0" sink="AlignLinear.StandardVolume_1" /> <connection source="SkullStrippedmousedataNORMAL.Output_0" sink="AlignLinear.ResliceVolume_1" /> <connection source="AlignLinear.LinearTransformation_1" sink="Reslice.Input.airLinearTransformation_1" /> <connection source="skullstrippedatlas.Output_0" sink="AlignLinear.StandardVolume_2" /> <connection source="skullstrippedatlasINJECTED.Output_0" sink="AlignLinear.ResliceVolume_2" /> <connection source="AlignLinear.LinearTransformation_2" sink="Reslice.Input.airLinearTransformation_2" /> <connection source="TrimImage.Outputimage_0" sink="Binarize.Input_0" /> <connection source="CompileFinalResults.PValuesImage_0" sink="BinaryMask.Input_0" /> <connection source="Binarize.OutputBinaryVolume_0" sink="BinaryMask.BinaryMaskFile_0" /> <connection source="BinaryMask.Outputmaskedvolume_0" sink="MaskedP-Values.Input_0" /> <connection source="KL_MI_register.displacementfieldimage_1" sink="InitializeStats.ControlsList_0" /> <connection source="KL_MI_register.displacementfieldimage_0" sink="InitializeStats.SubjectsList_0" /> <connection source="ProgramsFiles.Output_0" sink="InitializeStats.ExecutableDirectory_0" /> <connection source="Options.Output_0" sink="InitializeStats.Options_0" /> <connection source="KL_MI_register.displacementfieldimage_0" sink="ComputeDeformationTensors.InputList_0" /> <connection source="KL_MI_register.displacementfieldimage_1" sink="ComputeDeformationTensors.InputList_0" /> <connection source="ProgramsFiles.Output_0" sink="ComputeDeformationTensors.ExecutableDirectory_0" /> <connection source="InitializeStats.OutputDirectory_0" sink="ComputeDeformationTensors.OutputDirectory_0" /> <connection source="ProgramsFiles.Output_0" sink="ComputeVoxelwiseStatistics.ExecutableDirectory_0" /> <connection source="InitializeStats.OutputDirectory_0" sink="ComputeVoxelwiseStatistics.InputDirectory_0" /> <connection source="Options.Output_0" sink="ComputeVoxelwiseStatistics.Options_0" /> <connection source="Slices.Output_0" sink="ComputeVoxelwiseStatistics.iSlice_0" /> <connection source="ComputeDeformationTensors.Output_0" sink="ComputeVoxelwiseStatistics.SynchParameter_0" /> <connection source="InitializeStats.OutputDirectory_0" sink="CompileFinalResults.OutputDirectory_0" /> <connection source="ProgramsFiles.Output_0" sink="CompileFinalResults.Executionpath_0" /> <connection source="ComputeVoxelwiseStatistics.Output_0" sink="CompileFinalResults.DummySynch_0" /> <connection source="CompileFinalResults.PValuesImage_0" sink="Results.Input_0" /> <connection source="CompileFinalResults.TValuesImage_0" sink="Results.Input_0" /> <connection source="Reslice.OutputReslicedVolume_2" sink="KL_MI_register.Targetimage_0" /> <connection source="skullstrippedatlas.Output_0" sink="KL_MI_register.Templateimage_0" /> <connection source="Reslice.OutputReslicedVolume_1" sink="KL_MI_register.Targetimage_1" /> <connection source="skullstrippedatlas.Output_0" sink="KL_MI_register.Templateimage_1" /> <connection source="skullstrippedatlas.Output_0" sink="TrimImage.Inputimage_0" /> </connections> 10

  11. Executable Provenance Executable provenance Environment Options Input files Output files Binary provenance Binary configuration Configuration options System configuration Architecture Operating system Compiler Libraries Script provenance Shell Script Binary provenance 11

  12. Alignlinear Provenance <binary name="alignlinear" version="5.2.5" package="AIR" uri="http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8" compilationTime="2006-04-21T11:58:00"> <systemConfig> <architecture name="x86" vendor="Intel" model="T2400" processorFlags="" /> <OS name="MacOSX" version="10.5.3" distribution="" kernelName="Darwin" kernelVersion="9.3.0" /> <compiler name="GCC" version="4.0.1" flags="-o -Lsrc -lRPW -lm -g -02" updates="" /> </systemConfig> <configOptions> <config name="AIR_CONFIG_GROUPS" value="1" /> <config name="HAVE_LIBM" value="1" /> <config name="AIR_CONFIG_AUTO_BYTESWAP" value="1" /> <config name="AIR_CONFIG_REP16" value="1" /> <config name="AIR_CONFIG_VERBOSITY" value="0" /> <config name="AIR_CONFIG_DECOMPRESS_COMMAND" value="/usr/bin/gunzip -c" /> <config name="AIR_CONFIG_PIX_SIZE_ERR" value=".0001" /> <config name="AIR_CONFIG_THRESHOLD1" value="7000" /> <config name="AIR_CONFIG_OUTBITS" value="16" /> <config name="AIR_CONFIG_REQ_PERMS" value="2" /> <config name="AIR_CONFIG_THRESHOLD2" value="7000" /> <config name="AIR_CONFIG_PIPES" value="1" /> <config name="AIR_CONFIG_DECOMPRESS" value="1" /> <config name="AIR_CONFIG_PATHS" value="1" /> <config name="STDC_HEADERS" value="1" /> </configOptions> </binary> 12

  13. Reproducibility • Across Platform • ICA workflow • Across compilations • MDA workflow 13

  14. Independent Components Analysis 14

  15. Different Architectures Yield Different Results 15

  16. Minimum Deformation Atlas 16

  17. Different Compilation Options Yield Different Results 17

  18. Complex Neuroimaging Workflow 18

  19. Future Directions • Community involvement • provenance.loni.ucla.edu • Make LONI Pipeline aware of provenance files • Read in provenance file • Display executable provenance • Append provenance information • Write out provenance file • Visualize provenance files • Interface similar to LONI Pipeline • Invoke LONI Pipeline to recreate file or modify processing • Provenance Database • Database of workflows 19

  20. Acknowledgements • Arthur W. Toga • Director, Laboratory of Neuro Imaging • Arash Payan • Lead Developer, LONI Pipeline • Ivo D. Dinov • Assistant Professor, Laboratory of Neuro Imaging • John D. Van Horn • Assistant Professor, Laboratory of Neuro Imaging 20

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