Pinned Repositories
autobids
Automated Dicom to BIDS and pipelines using compute canada
bids-tutorial
Tutorial on BIDS - Methods Lunch Feb 12
hippunfold
BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
Khanlab_Tutorials
labelmerge
Merge label maps
mp2rage_correction
BIDS App for correction of residual B1 in MP2RAGE based on Sa2RAGE (code from JP Marques)
neuroglia-helpers
Helper and wrapper scripts for using Singularity locally and on compute canada
scattr
BIDS app for structural connectivity between targeted regions
snakebids
Snakemake + BIDS
tar2bids
Khan Computational Imaging Lab's Repositories
khanlab/hippunfold
BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
khanlab/snakebids
Snakemake + BIDS
khanlab/tar2bids
khanlab/autobids
Automated Dicom to BIDS and pipelines using compute canada
khanlab/scattr
BIDS app for structural connectivity between targeted regions
khanlab/labelmerge
Merge label maps
khanlab/SPIMprep
A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
khanlab/khanlab.github.io
Khan Lab website
khanlab/gcnn_dmri
khanlab/SPIMquant
SnakeBIDS app for quantitative analysis of SPIM (lightsheet) brain data
khanlab/subcorticalparc-smk
General-purpose Snakemake workflow for subcortical parcellation with functional and structural connectivity
khanlab/zarrnii
Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations
khanlab/actions
Centralized repo of reusable GH actions
khanlab/autobids-globus
Automatically manage globus distribution of Autobids datasets
khanlab/autobids-portal
khanlab/cvpl_tools
A Python package for utilities and classes related to the file I/O, dataset record keeping for image processing and computer vision.
khanlab/diffparc-surf
Snakebids app for diffparc-surf, including dwi processing
khanlab/eplink-redcap2bids
Workflow for exporting redcap braincode data to bids
khanlab/hippunfold-frozen-2024-04-25
Frozen archive of hippunfold (prior to rewriting history in hippunfold)
khanlab/hippunfold-train-finetune
Workflow for training nnUnet with pre-existing weights
khanlab/hippunfold_deps
Dependencies container for hippocampal_autotop (niftynet, minified fsl/ants, c3d, mcr)
khanlab/LOBE_analysis
Snakemake workflow for LOBE study
khanlab/SPIMprep-deps
khanlab/SPIMquant-deps
khanlab/spimquant_cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
khanlab/spimquant_CellSeg3D
A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks
khanlab/tar2bids-heuristics
Study heuristics for autobids
khanlab/trident-datamgmt-scripts
Various scripts for TRIDENT data management
khanlab/trident_example_project
khanlab/wiki