LNCD Tools

small scripts useful for data wrangling at the LNCD

Install

See the docs

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

• 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, melanin_align - modality specific wrappers

tat2

also see more detaied docs (/Volumes/Hera/Datasets/ABCD/TAT2/tat2_avg3797_med_voldisc.nii.gz and /Volumes/Hera/Projects/7TBrainMech/scripts/mri/tat2/mean_176.nii.gz)

permutation of tat2 calls were compared against R2 acquisitions: -vol_median is likely the approprate normalization.

(/Volumes/Phillips/mMR_PETDA/scripts/tat2/multiverse)

Notes

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