khanlab/prepT2space khanlab/prepT2space

  • Stars
    star
    1
  • Language
    Shell
  • Created almost 7 years ago
  • Updated over 6 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
khanlab/prepT2space
github

khanlab

Reviews

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

Repository Details

preprocessing for 7T 3D T2 SPACE data

More Repositories

1

hippunfold

BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
Python
47
star
2

snakebids

Snakemake + BIDS
Python
17
star
3

tar2bids

Python
7
star
4

autobids

Automated Dicom to BIDS and pipelines using compute canada
Shell
5
star
5

bids-tutorial

Tutorial on BIDS - Methods Lunch Feb 12
5
star
6

neuroglia-helpers

Helper and wrapper scripts for using Singularity locally and on compute canada
Shell
5
star
7

scattr

BIDS app for structural connectivity between targeted regions
Python
4
star
8

labelmerge

Merge label maps
Python
3
star
9

mp2rage_genUniDen

Generates UNI-DEN image from UNI, Inv1 and Inv2 images
MATLAB
3
star
10

mp2rage_correction

BIDS App for correction of residual B1 in MP2RAGE based on Sa2RAGE (code from JP Marques)
MATLAB
3
star
11

khanlab.github.io

Khan Lab website
HTML
2
star
12

cfmm2tar

Tools for dicom-server retrieval, tarballing and conversion to bids
Python
2
star
13

niftynet_hackathon

2
star
14

histmri

Scripts and pipelines for histology-MRI registration and histology processing
MATLAB
2
star
15

prepdwi

BIDS-app for pre-processing DWI (denoise, unring, top-up, eddy, bedpost.. )
MATLAB
2
star
16

funcmasker-flex

BIDS App for U-net brain masking of fetal bold MRI
Jupyter Notebook
2
star
17

cc-slurm

This profile configures Snakemake to run on Compute Canada with SLURM (e.g. graham).
Python
2
star
18

gradcorrect

BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correction fields
Shell
2
star
19

SPIMprep

A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
Python
2
star
20

hippunfold-templateflow

Hippunfold outputs on templateflow templates
1
star
21

dcmtk_pacs

Dockerfile
1
star
22

SPIMquant

SnakeBIDS app for quantiative analysis of SPIM (lightsheet) brain data
Jupyter Notebook
1
star
23

zarrnii

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations
Jupyter Notebook
1
star
24

gcnn_dmri

Python
1
star