LNCD Tools

A set of small data wrangling scripts at the LNCD.

Detailed information in the docs

Install

See the setup documentation.

Briefly clone and add to path

git clone https://github.com/lncd/lncdtools ~/lncdtools
echo "export PATH=\$PATH:$HOME/lncdtools" >> ~/.bashrc

Usage/cookbooks

• TODO: Makefile sentinels for make using mkifdiff, mkls, mkmissing, mkstat
• BIDS with dcmdirtab, dcmtab_bids, and mknii

Tools

• shell wrappers niinote, skip-exist, waitforjobs, dryrun, drytee
• tat2 (cf. dR2*), tsnr, melanin_align - modality specific wrappers
• 4dConcatSubBriks - extract a subbrick from a list of nifti label with luna ids. Useful for quality checking many structurals, subject masks, or individual contrasts. Wraps around 3dbucket and 3drefit:
• img_bg_rm - use imagemagick's convert to set a background to alpha (remove). Taken from "hackerb9" stack overflow solution. use on afni and suma screen captures
• mkmissing - find missing patterns between two steps in a pipeline (file globs)
• r - read dataframe from stdin and run R code with shortcuts and magic a la DataScienceToolkit's Rio

tat2

Tip

• tat2 is now (2026) dR2* and hosted https://github.com/Larsen-Lab/dR2star
• dR2* (née tat2) validation is also hosted in its own repository tat2-validation

Also see more detaied docs

Notes

• get_ld8_age.R requires R and the LNCDR package + access with the firewall (for db at arnold.wpic.upmc.edu)