Projects | Darren Liang

ASHS for SLURM

Mon, 09 May 2022 00:00:00 +0000

Simple script that points to the ASHS directory (containing bin and atlases), input directory (BIDS compliant), and output directory (usually derivatives folder), and submits ASHS_main.sh via. SLURM scheduler using regularInteractive provided by neuroglia-helpers (https://github.com/khanlab/neuroglia-helpers).

Automatic Segmentation of Hippocampal Subfields (ASHS) is developed by members of the Penn Image Computing and Science Laboratory (PICSL) at the Department of Radiology at the University of Pennsylvania (https://sites.google.com/site/hipposubfields/). Atlas version used (ashs_atlas_upennpmc_20161128) and all other ASHS scripts and functions is supported by their group and can be found at https://www.nitrc.org/frs/?group_id=370.

Framewise Displacement

Mon, 09 May 2022 00:00:00 +0000

Simple script that extracts the framewise displacement variable from fMRIPrep v20.0.1 confounds file which can be used with any BIDS compliant directory. Will take all subjects and all functional run types if fMRIPrep has produced a confound_timeseries.tsv file for. There isn’t an agreement on the limit of framewise displacement which should determine exclusion so currently script determines which subject runs exceeds the following framewise displacement values: 1mm, 1.1mm, 1.2mm, 1.5mm, 2mm, and max value but will only output excess of 1mm if save option is not enabled. Can be modified to extract any column of fMRIPrep confounds and used as a general value checker.

Ontario COVID-19

Fri, 15 Oct 2021 00:00:00 +0000

Advent of Code 2020 Day 1

Tue, 01 Dec 2020 00:00:00 +0000

Sample solution to the daily advent of code challenge from https://adventofcode.com/2020/day/1.

Personal puzzle input text file.