Ali Khan's repositories
marm94T-bids-smk
Snakemake workflow for converting 9.4T marmoset data to bids (for zona protocol with MP2RAGE, MTsat, DWI)
baby-shower
Baby shower website
batch-hippunfold
Snakemake workflow for batch job submission with hippunfold container
batch-snakedwi
Batch submit workflow for snakedwi
BigStitcher-Spark
Running compute-intense parts of BigStitcher distributed
clark_maguire_bidsify
BIDS conversion of Clark and Maguire 2023 dataset
DiffSimGen
DiffSimGen (Diffusion Simulator Generator)
example-snakebids
Minimalist snakemake+snakemake BIDS App
freesurfer_bidsapp
Snakebids app for Freesurfer
hippunfold-test
Run hippunfold version(s) on a subset of openneuro datasets for quantitative comparison
kslurm
Helper scripts and wrappers for running commands on SLURM compute clusters.
macbrain-downloader
Downloader for dzi images hosted on the web
macbrain-recon
Macaque brain reconstruction snakemake workflow
marm94T-gradients
Gradients analysis for marm zona project
neonatal-hippunfold-vis
Workflow for visualizing dHCP neonatal hippunfold data from the zip
open-science-benefits
Slides for August 9, 2022 talk on how you can benefit from open science practices
postproc-smk
WIP - Simple Post-BIDS processing pipeline with snakemake
pybids
Python tools for querying and manipulating BIDS datasets.
scattr
BIDS app for structural connectivity between targeted regions
scona
Code to analyse structural covariance brain networks using python.
snakeanat
snakeanat
snakebatch
Customizeable workflow for batching multiple snakebids apps or bids apps
snakeboost
Utility functions to turbocharge snakemake workflows
subj2bids
Simple workflow for single subject dicom archive to bids
SynthSR
A framework for joint super-resolution and image synthesis, without requiring real training data