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LORIS Imaging Preprocessing Pipeline 15.10
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@driusan driusan released this 15 Dec 17:47
v15.10
cbd0dfd

New Features

  • NifTI conversion: Imaging pipeline can automatically generate NifTI in addition to MINC format for all incoming DICOM volumes
  • PET insertion supported

Notes for existing projects

  • Tarchive path is now relative in the tarchive table. Requires updating the dicom-archive-tool repository, and running its MakeArchiveLocationRelative.pl script
  • ClassifyAlgorithm field removed from imaging file metadata
  • prod config file updates:
    • line 33: set $bin_dir variable to directory where Loris-MRI code is installed
    • Recommended: add NifTI conversion parameter $no_nii = 0; (or =1 to use NifTI)
  • environment config file: set $LORIS_CONFIG variable to dicom-archive directory

Caveats / Known Issues

  • Install the latest stable minc toolkit available from the BIC website to resolve the following errors thrown by the imaging pipeline:
    • mincpik: Failed executing mincreshape due to Segmentation fault in mincreshape
    • make_jiv error due to missing utilities: Can't locate auto/MNI/MincUtilities/volume_para.al in @ INC ... at /data/$proj/bin/mri/uploadNeuroDB/bin/minc2jiv.pl line 124
      To update your minc toolkit:
    • sudo apt-get remove minc-tools (to remove minc tools installed by imaging_install.sh)
    • Download and follow instructions on the BIC website to install dependencies and the minc toolkit, and update your .bashrc
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