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
snakedwi
wb-cifti-tutorial
Connectome workbench & GIFTI/CIFTI tutorial
akhanf's Repositories
akhanf/MDT
Microstructure Diffusion Toolbox
akhanf/vasst-dev
Dev tools for vasst pipeline
akhanf/ants_build_template_smk
Snakemake workflow for building an ANTS template (from antsMultivariateTemplateConstruction2.sh)
akhanf/aoc2018
akhanf/aoc2020
advent of code
akhanf/avgRuns
pipeline for motion-correcting and averaging runs
akhanf/avgRuns_smk
Snakemake workflow for register and avg runs from a bids dataset
akhanf/CCCVTK
The Canadian Common CV Toolkit
akhanf/circle-ci
example builder for Singularity containers using Circle Continuous Integration, circle-ci
akhanf/clinical-atlasreg
akhanf/dna-seq-varlociraptor
Variant detection with Delly and Freebayes, followed by statistical assessment with Varlociraptor
akhanf/freesurfer
recon-all from FreeSurfer
akhanf/giraffe_test
akhanf/github-ci
An example GitHub Action (CI) to build a Singularity container
akhanf/gradcorrect
BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correction fields
akhanf/hello-github-actions
akhanf/Hippocampal_AutoTop
akhanf/misc_notebooks
Miscellaneous notebooks for BIDS, image processing, QC etc..
akhanf/my_bids_app
akhanf/piriform-diffparc
Diffusion parcellation of piriform cortex snakemake workflow
akhanf/postmortem-7T-preproc
Pre-processing for post-mortem whole brain 7T data (Khan/Duerden)
akhanf/qsm_sstv
BIDS app for single step total variation QSM processing of Siemens 7T data
akhanf/reflection-in-Qt
akhanf/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
akhanf/SnakeChunks
Modular blocks to build Snakemake workflows for reproducible NGS analyses
akhanf/snakemake-neuroimaging-intro
Some slides introducing Snakemake for neuroimaging (WIP!)
akhanf/snakemake_hippocampal_unfolding
akhanf/snakemake_neuroworkflow
Template repository for snakemake neuroimaging workflows
akhanf/structural_connectome_smk
Snakemake workflow for structural connectome using mrtrix3 (loading BIDS data from prepdwi, fmriprep)
akhanf/zona-diffparc