khanlab/autobids

This repository has been archived on 13/Jun/2024
Stars
5
Rank 2,851,595 (Top 57 %)
Language
Shell
Created almost 7 years ago
Updated 4 months ago

khanlab/autobids

khanlab

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Automated Dicom to BIDS and pipelines using compute canada

hippunfold

BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

snakebids

Snakemake + BIDS

tar2bids

bids-tutorial

Tutorial on BIDS - Methods Lunch Feb 12

neuroglia-helpers

Helper and wrapper scripts for using Singularity locally and on compute canada

scattr

BIDS app for structural connectivity between targeted regions

Khanlab_Tutorials

labelmerge

Merge label maps

mp2rage_genUniDen

Generates UNI-DEN image from UNI, Inv1 and Inv2 images

mp2rage_correction

BIDS App for correction of residual B1 in MP2RAGE based on Sa2RAGE (code from JP Marques)

khanlab.github.io

Khan Lab website

cfmm2tar

Tools for dicom-server retrieval, tarballing and conversion to bids

niftynet_hackathon

histmri

Scripts and pipelines for histology-MRI registration and histology processing

prepdwi

BIDS-app for pre-processing DWI (denoise, unring, top-up, eddy, bedpost.. )

funcmasker-flex

BIDS App for U-net brain masking of fetal bold MRI

Jupyter Notebook

cc-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 fields

SPIMprep

A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)

hippunfold-templateflow

Hippunfold outputs on templateflow templates

prepT2space

preprocessing for 7T 3D T2 SPACE data

dcmtk_pacs

SPIMquant

SnakeBIDS app for quantiative analysis of SPIM (lightsheet) brain data

Jupyter Notebook

zarrnii

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

Jupyter Notebook

gcnn_dmri