97 Works

LiFE and AFQ Quality Check

Lindsey Kitchell & Daniel Bullock
Generates multiple graphs that can be used as a quality check for the outputs of AFQ and LiFE. This application will only work if the zero weighted fibers are removed AFTER AFQ.

rsHRF

Soichi Hayashi, Sofie Van Den Bossche, Madhur Tandon, Guorong Wu, Franco Pestilli & Daniele Marinazzo
Hemodynamic Response Function Retrieval and Deconvolution (RS-HRF)

AFQ Tract Classification with LiFE

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service uses Automated fiber quantification AFQ and fe structure output from LiFE to identify major tract segments and quantify tissue properties along their trajectories. You can choose to have the zero weighted fibers (as determined by LiFE) removed before or after AFQ is applied. useinterhemisphericsplit is a variable from AFQ, which if set to true will cut fibers crossing between hemispheres with a midsaggital plane below z=-10. This is to get rid of CST...

TractSeg training

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

Map pRFs in visual cortex with anatomy

David Hunt
Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

Steklov Operator Spectrum

Lindsey Kitchell
app to calculate the Steklov Operator Spectrum on 3D surfaces

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.

Align HCP to Native Space

David Hunt
Aligns HCP fMRI data in MNI space to subject space

Freesurfer Deface

Soichi Hayashi
Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca

wmaSeg - Giulia's patch

Giulia Berto
Classifies streamlines into known anatomical tracts.

Convert wmc-deprecated to wmc

Giulia Berto
App to convert the old wmc-deprecated datatype to the new wmc datatype

Tractography quality check

Daniel Bullock
A quality check application for tractography, segmentatations, and LiFE structures. For the whole brain tractogram, provides a number of statistics associated with average streamline characteristics (i.e. count, volume occupied, avg length, length distribution). Does the same for the positively weighted streamlines of an FE structure if input. If a classification structure is input, provides a number of macrostructural statistics like stream count, volume, avg length, whole brain count/volume proportion, etc).

White matter tracts statistics and quality control

Franco Pestilli & Daniel Bullock
This brainlife.io App will compute aggregrate statistics on the white matter tracts produced on brainlife.io. Statistics such as fiber count, tract volume, etc can be used to compare across tracts, across subjects either for scientific analyses or quality control of the results.

Generate tract endpoint maps (new wmc Input)

Daniel Bullock
This app will generate endpoint maps for all tracts in an input classification structure. User can specify what sort of decay/smoothing algorithm can be used (or none).

Tractography quality check

Daniel Bullock
A quality check application for tractography, segmentatations, and LiFE structures

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.

FSL Brain Extraction (BET) on DWI

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

ANTs tractogram registration in MNI space

Giulia Berto
ANTs transformation based on T1 and tractogram registration in MNI space

Remove First B0 (temp)

Brad Caron
Temporary app to remove first b0 for Athlete Brain Study Dataset

Segment tractogram into fiber categories

Franco Pestilli & Daniel Bullock
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).

app-repeat-network-osg

Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

AFQ Tract Classification

Soichi Hayashi & Lindsey Kitchell
This service uses Automated fiber quantification AFQ and fe structure output from LiFE to identify major tract segments and quantify tissue properties along their trajectories. You can choose to have the zero weighted fibers (as determined by LiFE) removed before or after AFQ is applied. useinterhemisphericsplit is a variable from AFQ, which if set to true will cut fibers crossing between hemispheres with a midsaggital plane below z=-10. This is to get rid of CST...

Registration Year

  • 2019
    97

Resource Types

  • Software
    97