Pinned Repositories
cookiecutter-snakebids
Cookiecutter template for a Python package.
denoise-fmri
Snakemake BIDS app for denoising fmriprep, uses the snakebids package for running snakemake workflow as bids app
freesurfer_subfields_bids
SnakeBIDS app for freesurfer hippocampal subfield segmentation
marm94T-bids-smk
Snakemake workflow for converting 9.4T marmoset data to bids (for zona protocol with MP2RAGE, MTsat, DWI)
MDT
Microstructure Diffusion Toolbox
methods-lunch-spatial-normalization
Methods lunch (Feb 14, 2022) on spatial normalization
MP2RAGE-related-scripts
MP2RAGE Scripts - T1 map correction & Background noise removal
nnunet-fetalbrain
nnUnet training workflow for fetal bold MRI
wb-cifti-tutorial
Connectome workbench & GIFTI/CIFTI tutorial
akhanf's Repositories
akhanf/snakebids
Snakemake + BIDS
akhanf/snakedwi
akhanf/marm94T-bids-smk
Snakemake workflow for converting 9.4T marmoset data to bids (for zona protocol with MP2RAGE, MTsat, DWI)
akhanf/baby-shower
Baby shower website
akhanf/batch-snakedwi
Batch submit workflow for snakedwi
akhanf/BigStitcher-Spark
Running compute-intense parts of BigStitcher distributed
akhanf/canbind2bids
akhanf/clark_maguire_bidsify
BIDS conversion of Clark and Maguire 2023 dataset
akhanf/compare_spiral_dwi
Snakemake workflow for comparing 7T spiral vs non-spiral dwi
akhanf/conda-snakebids-builds
assortment of conda build files to get snakebids built
akhanf/DiffSimGen
DiffSimGen (Diffusion Simulator Generator)
akhanf/freesurfer_bidsapp
Snakebids app for Freesurfer
akhanf/hippunfold-test
Run hippunfold version(s) on a subset of openneuro datasets for quantitative comparison
akhanf/hippunfold_synthseg_hcp
akhanf/kslurm
Helper scripts and wrappers for running commands on SLURM compute clusters.
akhanf/LOBE_preprocessing
Snakebatch pre-processing for LOBE study
akhanf/macbrain-downloader
Downloader for dzi images hosted on the web
akhanf/macbrain-recon
Macaque brain reconstruction snakemake workflow
akhanf/marm94T-gradients
Gradients analysis for marm zona project
akhanf/neonatal-hippunfold-vis
Workflow for visualizing dHCP neonatal hippunfold data from the zip
akhanf/open-science-benefits
Slides for August 9, 2022 talk on how you can benefit from open science practices
akhanf/postproc-smk
WIP - Simple Post-BIDS processing pipeline with snakemake
akhanf/pybids
Python tools for querying and manipulating BIDS datasets.
akhanf/scattr
BIDS app for structural connectivity between targeted regions
akhanf/scona
Code to analyse structural covariance brain networks using python.
akhanf/snakeanat
snakeanat
akhanf/snakebatch
Customizeable workflow for batching multiple snakebids apps or bids apps
akhanf/snakeboost
Utility functions to turbocharge snakemake workflows
akhanf/snakemake-executor-plugin-googlebatch
Snakemake executor plugin for Google Batch (under development)
akhanf/subj2bids
Simple workflow for single subject dicom archive to bids