khanlab/SPIMquant

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Created 8 months ago
Updated 17 days ago

khanlab/SPIMquant

khanlab

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

hippunfold

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

snakebids

Snakemake + BIDS

tar2bids

autobids

Automated Dicom to BIDS and pipelines using compute canada

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

zarrnii

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

Jupyter Notebook

gcnn_dmri