244 Works

DSC evaluation (mask - mask)

Giulia Berto
Compute the Dice Similarity Coefficient (DSC) between corresponding tracts of the given segmentation and the ground truth when using HCP data.

Dipy Info

Soichi Hayashi, Serge Koudoro & Aman Arya
Provides useful information about different files used in medical imaging.

TractSeg training

Pietro Astolfi, Paolo Avesani & Giulia Berto
Automatic White Matter Bundle Segmentation

TractSeg

Soichi Hayashi, Lindsey Kitchell & Jakob Wasserthal
Brainlife App for MIC-DKFZ/TractSeg. A tool for fast and accurate white matter bundle segmentation from Diffusion MRI using pretrained pytorch ML model.

FSL Brain Extraction (BET) on T2

Lindsey Kitchell & Brad Caron
Brain Extraction via FSL's BET command

Plot tract measures

Giulia Berto
Compute and plot total number of fibers, total number of nodes and average length of some tracts.

Reslice

Soichi Hayashi & Serge Koudoro
Reslice a dMRI dataset to have isotropic voxel size (dipy_reslice)

LAP multiple examples with LiFE

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

CSA Peaks

Aman Arya
This service generates a csa model using dipy from a given dwi file and freesurfer mask. It then saves the evaluated peaks of the csa model into a dipy compatible .pam5 (peaks and models 5) file type for use in other dipy applications and scripts.

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Shape Signature

Soichi Hayashi
This App takes tract masks and convert them to series of numerical values that chracaterizes each masks. The numerical values are generated from the flattened output of 3D convolutional layers of the model trained to classify tract names. Output values could be used as a "shape signature" and compared against other similar shaped tracts.

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

TractSeg

Soichi Hayashi, Lindsey Kitchell & Jakob Wasserthal
Brainlife App for MIC-DKFZ/TractSeg. A tool for fast and accurate white matter bundle segmentation from Diffusion MRI using pretrained pytorch ML model.

NODDI Amico (single shell)

Brad Caron
This fits the NODDI model on single shell data. The only value that should be trusted is orientation dispersion (OD), as this measure can be fit accurately with single shell data

test

Brad Caron
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

fMRIPrep

Daniel Levitas, David Hunt, Josh Faskowitz & Soichi Hayashi
runs fmriprep for brainlife

Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation

Paolo Avesani & Giulia Berto
A benchmark to test a tract segmentation method that takes into account information about both the underlying anatomy and the geometry of bundles at the same time.

Posterior Associative White Matter Tracts Segmentation

Franco Pestilli & Daniel Bullock
This brainlife.io App implements the white matter segmentation of the vertical tracts described in Bullock et al. 2019. It segments 8 (4 per hemisphere) white matter tracts, the posterior Arcuate (pArc), temporal-parietal connection (TPC), middle-longitudinal fasciculus (MdLF-SPL MdLF-Ang) and the vertical occipital fasciculus (VOF).

Freesurfer Group Analysis

Soichi Hayashi
Do some basic group analysis on freesurfer outputs

Plot 3D Surfaces

Lindsey Kitchell
This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.

multi-LAP

Giulia Berto
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).

Diffusion Predictor Grid Search (AppA) (old)

Soichi Hayashi
This is an old version that used dwi instead of dtiinit

Registration Year

  • 2018
    140
  • 2019
    104

Resource Types

  • Software
    244