List of data that are removed

[tashrifbillah]

HCP pipeline does not remove them but for disk usage optimization at PNL, we do:

• eddy_unwarped_images.eddy_outlier_free_data.nii.gz
  

  HCPpipelines/DiffusionPreprocessing/scripts/run_eddy.sh

  Line 624 in 9fa236c

  ${FSLDIR}/bin/imrm ${workingdir}/eddy_unwarped_images.eddy_outlier_free_data

• rawdata
  

  HCPpipelines/DiffusionPreprocessing/scripts/run_eddy.sh

  Line 627 in 9fa236c

  rm -r ${workingdir}/../rawdata

• intensity normalized data
  

  HCPpipelines/DiffusionPreprocessing/scripts/run_eddy.sh

  Line 646 in 9fa236c

  rm ${workingdir}/Pos_Neg.nii.gz

• wo_repol_outDir
  

  HCPpipelines/DiffusionPreprocessing/scripts/eddy_pnl_repol.py

  Line 78 in 9fa236c

  check_call(f'rm -r {wo_repol_outDir}', shell=True)

[tashrifbillah]

HCPpipelines/DiffusionPreprocessing/scripts/run_eddy.sh

Line 646 in 93a5964

rm ${workingdir}/Pos_Neg.nii.gz

Undo this removal maybe, otherwise it is hard to debug afterward.