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/denoise-fmri
Snakemake BIDS app for denoising fmriprep, uses the snakebids package for running snakemake workflow as bids app
akhanf/methods-lunch-spatial-normalization
Methods lunch (Feb 14, 2022) on spatial normalization
akhanf/app-hippunfold-t1
Brainlife app for hippunfold
akhanf/greedy_template_marm
marmoset template building WIP
akhanf/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
akhanf/hippunfold-plan-refactor
file lists to help plan hippunfold file/folder structure refactoring
akhanf/nnunet-fetalbrain
nnUnet training workflow for fetal bold MRI
akhanf/snakebids-tutorial-data
Snakebids tutorial (WIP)
akhanf/prep_retraining_dwi_hippunfold_smk
Snakemake workflow for pre-processing dwi data to re-train using b1000 hcp data
akhanf/consensus_study_snakedwi
workflow for processing ISMRM Diffusion Study - Best Practices in Image Preprocessing data
akhanf/preprocgre_bruker
Workflow for pre-processing Bruker 9.4T GRE scans
akhanf/sftp-jailed-sshfs
Scripts for setting up jailed sftp server, with sshfs mounted shares
akhanf/hcp-lifespan-downloader
Snakemake workflow for downloading HCP Lifespan data
akhanf/basalfb-diffparc
akhanf/hippdwi_HcECT
Registration and metric extraction for low-bval DWI (requires hippunfold, and prepdwi --no-regT1)
akhanf/stardist_smk
Stardist snakemake workflow
akhanf/tract-fconn-smk
Tract-weighted functional connectivity snakemake workflow - WIP
akhanf/wb-cifti-tutorial
Connectome workbench & GIFTI/CIFTI tutorial
akhanf/nnUNet
akhanf/Deep-MRI-Reconstruction
Deep Cascade of Convolutional Neural Networks for MR Image Reconstruction: Implementation & Demo
akhanf/app-fmriprep
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
akhanf/snakebids2dicom
snakebids2dicom
akhanf/brainlife-computecanada
Docs and readme for setting up Brainlife with Compute Canada
akhanf/cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows
akhanf/snakebids-app
DEPRECATED - Cookiecutter template for creating a Snakebids BIDS App
akhanf/vimrc
The ultimate Vim configuration (vimrc)
akhanf/mdt_smk
Snakemake workflow for MDT
akhanf/equivariant-deep-dmri
Rotationally and translationally equivariant layers and networks for deep learning on diffusion MRI scans
akhanf/cookiecutter-snakebids
Cookiecutter template for a Python package.
akhanf/snakebids_boilerplate