akhanf/BigStitcher-Spark Fork of JaneliaSciComp/BigStitcher-Spark

Running compute-intense parts of BigStitcher distributed

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akhanf/LOBE_preprocessing

Snakebatch pre-processing for LOBE study

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akhanf/freesurfer_bidsapp

Snakebids app for Freesurfer

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akhanf/neuroglia-vasst-dev Fork of khanlab/neuroglia

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akhanf/freesurfer Fork of bids-apps/freesurfer

recon-all from FreeSurfer

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akhanf/greedy_template_camcan

template building for cam-can dataset

Language: Python - Size: 118 MB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 2

akhanf/github-ci Fork of singularityhub/github-ci

An example GitHub Action (CI) to build a Singularity container

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akhanf/funcmasker-compare

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akhanf/neonatal-hippunfold-vis

Workflow for visualizing dHCP neonatal hippunfold data from the zip

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akhanf/tar2bids2preproc-7T-extend

Template for extending the tar2bids2preproc-7T workflow

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akhanf/vimrc Fork of amix/vimrc

The ultimate Vim configuration (vimrc)

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akhanf/tract-fconn-smk

Tract-weighted functional connectivity snakemake workflow - WIP

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akhanf/test_datalad

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akhanf/vasst-dev

Dev tools for vasst pipeline

Language: Matlab - Size: 236 MB - Last synced: 3 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 3

akhanf/tar2bids2preproc-7T

Snakemake+snakebids pre-processing pipeline for 7T MRI

Language: Python - Size: 12.7 KB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

akhanf/SynthSR Fork of BBillot/SynthSR

A framework for joint super-resolution and image synthesis, without requiring real training data

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akhanf/surf_striatum

Pipeline for surface-based connectivity and morphometry in the striatum

Language: Matlab - Size: 299 MB - Last synced: 3 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

akhanf/SynthSeg Fork of BBillot/SynthSeg

Contrast-agnostic segmentation of MRI scans

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akhanf/structural_connectome_smk

Snakemake workflow for structural connectome using mrtrix3 (loading BIDS data from prepdwi, fmriprep)

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akhanf/snakemake_neuroworkflow

Template repository for snakemake neuroimaging workflows

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akhanf/snakemake_hippocampal_unfolding Fork of myousif9/Hippocampal-Autotop-vis

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akhanf/stardist_smk

Stardist snakemake workflow

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akhanf/snakemake-neuroimaging-intro Fork of yhatt/marp-cli-example

Some slides introducing Snakemake for neuroimaging (WIP!)

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akhanf/snakemake Fork of snakemake/snakemake

This is the development home of the workflow management system Snakemake. For general information, see

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akhanf/SnakeChunks Fork of SnakeChunks/SnakeChunks

Modular blocks to build Snakemake workflows for reproducible NGS analyses

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akhanf/snakebids2dicom Fork of tkkuehn/snakebids2dicom

snakebids2dicom

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akhanf/snakebids-app

DEPRECATED - Cookiecutter template for creating a Snakebids BIDS App

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akhanf/snakebids_boilerplate

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akhanf/snakebids-tutorial-data Fork of snakemake/snakemake-tutorial-data

Snakebids tutorial (WIP)

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akhanf/scratch-the-dura Fork of brainhack101/scratch-the-dura

Begin to learn how to leverage Git, Docker, Jupyter, and various neuroinformatics tools for performing exciting science!

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akhanf/sftp-jailed-sshfs

Scripts for setting up jailed sftp server, with sshfs mounted shares

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akhanf/rna-seq-star-deseq2 Fork of snakemake-workflows/rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

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akhanf/reflection-in-Qt Fork of parsley72/reflection-in-Qt

Size: 625 KB - Last synced: 3 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

akhanf/qsm_sstv Fork of AlanKuurstra/qsm_sstv

BIDS app for single step total variation QSM processing of Siemens 7T data

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akhanf/remote-cc-tools

some tools for accessing compute canada resources remotely

Language: Python - Size: 13.7 KB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 2

akhanf/pypmi Fork of rmarkello/pypmi

A very small toolbox for working with data from the Parkinson's Progression Markers Initiative (PPMI)

Language: Python - Size: 156 KB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

akhanf/prep_retraining_dwi_hippunfold_smk

Snakemake workflow for pre-processing dwi data to re-train using b1000 hcp data

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akhanf/presurfer-smk

Snakebids app for presurfer

Language: Python - Size: 58.6 KB - Last synced: 3 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

akhanf/preprocgre_bruker

Workflow for pre-processing Bruker 9.4T GRE scans

Language: Python - Size: 7.81 KB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

akhanf/open-science-benefits

Slides for August 9, 2022 talk on how you can benefit from open science practices

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akhanf/postmortem-7T-preproc

Pre-processing for post-mortem whole brain 7T data (Khan/Duerden)

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akhanf/piriform-diffparc

Diffusion parcellation of piriform cortex snakemake workflow

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akhanf/noelTexturesPy_wrapper

Singularity wrapper for noelTexturesPy

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akhanf/nnunet-fetalbrain

nnUnet training workflow for fetal bold MRI

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akhanf/nnUNet Fork of yinglilu/nnUNet

Size: 1.17 MB - Last synced: 3 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

akhanf/nipype Fork of nipy/nipype

Workflows and interfaces for neuroimaging packages

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akhanf/my_bids_app

Language: Python - Size: 4.88 KB - Last synced: 3 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

akhanf/mtl-histology-smk

Snakemake workflow for MTL histology data (curation, registration, quantification, ...)

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akhanf/MP2RAGE-related-scripts Fork of JosePMarques/MP2RAGE-related-scripts

MP2RAGE Scripts - T1 map correction & Background noise removal

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akhanf/misc_notebooks

Miscellaneous notebooks for BIDS, image processing, QC etc..

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akhanf/methods-lunch-spatial-normalization

Methods lunch (Feb 14, 2022) on spatial normalization

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akhanf/mdt-singularity

Singularity recipe for Microstructure Diffusion Toolbox (http://mdt-toolbox.readthedocs.io/en/latest/index.html)

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akhanf/marm94T-gradients

Gradients analysis for marm zona project

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akhanf/mdt_smk

Snakemake workflow for MDT

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akhanf/MAGeTbrain Fork of bids-apps/MAGeTbrain

Language: Python - Size: 25.4 KB - Last synced: 3 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

akhanf/khanlab-osf Fork of myousif9/khanlab-osf

Size: 2.68 MB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

akhanf/macbrain-recon

Macaque brain reconstruction snakemake workflow

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akhanf/hist-mri_cadaver

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akhanf/HippUnfolding Fork of jordandekraker/HippUnfolding

Code for unfolding of hippocampal grey matter using Laplacian equation. Requires manual labelling of the hippocampal 'dark band' and grey matter, as well as some surrounding structures (see associated publication for instructions)

Language: Matlab - Size: 3.08 MB - Last synced: 3 days ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

akhanf/fmriprep Fork of nipreps/fmriprep

fMRIprep is a functional magnetic resonance image pre-processing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

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akhanf/hippunfold-plan-refactor

file lists to help plan hippunfold file/folder structure refactoring

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akhanf/hippunfold_toolbox Fork of myousif9/hippunfold_toolbox

Size: 8.41 MB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

akhanf/greedy_template_marm

marmoset template building WIP

Language: Python - Size: 118 MB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

akhanf/fslsnaps-smk

Snakemake workflow for fsleyes segmentation snapshots

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akhanf/giraffe_test

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akhanf/hippunfold_synthseg_hcp

Language: Python - Size: 8.79 KB - Last synced: 3 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

akhanf/global2017 Fork of brainhackorg/global2017

webpage for Brainhack Global 2017

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akhanf/hippunfold-test

Run hippunfold version(s) on a subset of openneuro datasets for quantitative comparison

Language: Python - Size: 1.95 KB - Last synced: 3 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

akhanf/gradcorrect Fork of khanlab/gradcorrect

BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correction fields

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akhanf/Hippocampal_AutoTop Fork of jordandekraker/Hippocampal_AutoTop

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akhanf/hello-github-actions

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akhanf/hippunfold-fs-ashs-comparison

Volumetric comparison of hippunfold with FS and ASHS

Language: Jupyter Notebook - Size: 650 MB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

akhanf/hippdwi_HcECT

Registration and metric extraction for low-bval DWI (requires hippunfold, and prepdwi --no-regT1)

Language: Python - Size: 1.95 KB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

akhanf/fetal-code Fork of saigerutherford/fetal-code

Automated Preprocessing Pipeline for Fetal Resting-State fMRI Data

Language: Jupyter Notebook - Size: 471 MB - Last synced: 3 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

akhanf/example-snakebids

Minimalist snakemake+snakemake BIDS App

Language: Python - Size: 31.3 KB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 2

akhanf/dna-seq-varlociraptor Fork of snakemake-workflows/dna-seq-varlociraptor

Variant detection with Delly and Freebayes, followed by statistical assessment with Varlociraptor

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akhanf/diffparc-smk

General-purpose Snakemake workflow for diffusion-based subcortical parcellation

Language: Python - Size: 1.4 MB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 7

akhanf/example-snakebids-simple

Simple bare-bones snakebids+snakemake workflow example (not a BIDS app)

Language: Python - Size: 8.79 KB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

akhanf/cookiecutter-snakebids Fork of audreyfeldroy/cookiecutter-pypackage

Cookiecutter template for a Python package.

Language: Python - Size: 525 KB - Last synced: 3 days ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

akhanf/equivariant-deep-dmri Fork of philip-mueller/equivariant-deep-dmri

Rotationally and translationally equivariant layers and networks for deep learning on diffusion MRI scans

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akhanf/core Fork of khanlab/core

Language: Python - Size: 35.2 KB - Last synced: 3 days ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

akhanf/Deep-MRI-Reconstruction Fork of js3611/Deep-MRI-Reconstruction

Deep Cascade of Convolutional Neural Networks for MR Image Reconstruction: Implementation & Demo

Language: Python - Size: 55 MB - Last synced: 3 days ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

akhanf/consensus_study_snakedwi

workflow for processing ISMRM Diffusion Study - Best Practices in Image Preprocessing data

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akhanf/cookiecutter-snakemake-workflow Fork of snakemake-workflows/cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

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akhanf/clinical-atlasreg

Language: Python - Size: 63.1 MB - Last synced: 3 days ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

akhanf/CCCVTK Fork of sylvainhalle/CCCVTK

The Canadian Common CV Toolkit

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akhanf/cbrain-plugins-neuro Fork of aces/cbrain-plugins-neuro

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akhanf/brainlife-computecanada

Docs and readme for setting up Brainlife with Compute Canada

Size: 2.93 KB - Last synced: 3 days ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

akhanf/basalfb-diffparc

Language: Python - Size: 1.95 MB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

akhanf/circle-ci Fork of singularityhub/circle-ci

example builder for Singularity containers using Circle Continuous Integration, circle-ci

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akhanf/avgRuns

pipeline for motion-correcting and averaging runs

Language: Python - Size: 17.6 KB - Last synced: 3 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

akhanf/brainstat_luciana

Language: Jupyter Notebook - Size: 813 KB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

akhanf/bids-apps.github.io Fork of bids-apps/bids-apps.github.io

Portable neuroimaging pipelines that understand BIDS datasets

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akhanf/batch-snakedwi

Batch submit workflow for snakedwi

Language: Python - Size: 16.6 KB - Last synced: 3 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

akhanf/app-hippunfold-t1

Brainlife app for hippunfold

Language: Shell - Size: 11.7 KB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

akhanf/ashs-bids

SnakeBIDS app for ASHS hippocampal subfield segmentation

Language: Python - Size: 6.84 KB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

akhanf/biomarkerproject

Size: 19.5 KB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

akhanf/avgRuns_smk

Snakemake workflow for register and avg runs from a bids dataset

Language: Python - Size: 2.93 KB - Last synced: 3 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

akhanf/aoc2020

advent of code

Language: Python - Size: 0 Bytes - Last synced: 3 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

akhanf/aoc2018

Language: Python - Size: 56.6 KB - Last synced: 3 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0