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