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hippunfold
BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)snakebids
Snakemake + BIDStar2bids
autobids
Automated Dicom to BIDS and pipelines using compute canadabids-tutorial
Tutorial on BIDS - Methods Lunch Feb 12neuroglia-helpers
Helper and wrapper scripts for using Singularity locally and on compute canadascattr
BIDS app for structural connectivity between targeted regionslabelmerge
Merge label mapsmp2rage_genUniDen
Generates UNI-DEN image from UNI, Inv1 and Inv2 imagesmp2rage_correction
BIDS App for correction of residual B1 in MP2RAGE based on Sa2RAGE (code from JP Marques)khanlab.github.io
Khan Lab websitecfmm2tar
Tools for dicom-server retrieval, tarballing and conversion to bidsniftynet_hackathon
histmri
Scripts and pipelines for histology-MRI registration and histology processingprepdwi
BIDS-app for pre-processing DWI (denoise, unring, top-up, eddy, bedpost.. )funcmasker-flex
BIDS App for U-net brain masking of fetal bold MRIcc-slurm
This profile configures Snakemake to run on Compute Canada with SLURM (e.g. graham).gradcorrect
BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correction fieldsSPIMprep
A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)hippunfold-templateflow
Hippunfold outputs on templateflow templatesprepT2space
preprocessing for 7T 3D T2 SPACE datadcmtk_pacs
SPIMquant
SnakeBIDS app for quantiative analysis of SPIM (lightsheet) brain datazarrnii
Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformationsLove Open Source and this site? Check out how you can help us