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UKButil

Utilities to share between fMRIB and BDI compute environments.

Set global environmental variable for each site. In FMRIB:

export UKB_SMS=/vols/Data/ukbiobank/FMRIB/SMS
export UKB_SUBJECTS=/vols/Data/ukbiobank/FMRIB/IMAGING/data3
export UKB_SCRIPTS=/vols/Scratch/ukbiobank/nichols/SCRIPTS
export UKB_TEMPLATES=/vols/Scratch/ukbiobank/nichols/TEMPLATES

In BDI

export UKB_SMS=/well/nichols/projects/UKB/SMS
export UKB_SUBJECTS=/well/win-biobank/projects/imaging/data/data3
export UKB_SCRIPTS=/well/nichols/scripts
export UKB_TEMPLATES=/well/nichols/scripts/TEMPLATES

Scripts for selecting/processing files

  • UKBfindVBM.sh: Find all subjects with VBM data; basically a find one-liner.

  • UKBsmoothVBM.sh: [FMRIB-specific! Needs updating!] Apply smoothing to VBM outputs.

  • Run_WarpfMRI-1.sh: Create command files and launch fsl_sub to complete warping, calling UKBwarp_tfMRI.sh.

  • Run_WarpfMRI-2.sh: QC/post processsing: Create count mask, run slicesdir, compute 1-sample t-test.

  • UKBwarp_tfMRI.sh: Run apply warp for a given task fMRI FEAT results directory.

Utility function (functions to be run once, or only infrequently)

  • ConvCategories.sh: Converts from a one-category-per-column format used at UKB Rodeo to the current ukbparse format.
  • UKBscrape.sh: Pull all possible field (variable) ID's from the UKB Showcase website.

FMRIB-only files, OLD... don't use for now

  • UKBclonefMRI-Run.sh
  • UKBclonefMRI.sh