138 Works

NODDI Amico (single shell) - Deprecated

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

mrtrix3-preproc-impr

Robert Puzniak
Improved version of the mrtrix3-preproc script deployed on BrainLife platform

Freesurfer on OSG

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Submit Freesurfer workflow on Open Science Grid (A national, distributed computing partnership for data-intensive research)

Track The Human Optic RAdiation (THORA): Contrack - Eccentricity

Brad Caron & Soichi Hayashi
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Convert wmc to trk

Soichi Hayashi
Convert a white matter classification (wmc) structure to a tractogram as a single trk file. Segmentation ID will be used to set bundle_code inside the .trk. You can access it with trk.tractogram.data_per_streamline[0]["bundle_code"] with nibabel

hello-world

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Generate ROIs in DMRI Space

Brad Caron
This app will generate ROIs from a parcellation, subcortical structures found in the Freesurfer aseg, cortical structures found in the Freesurfer parcellations, and population receptive field visual area segmentations. The ROIs will be resliced into diffusion space in of this, merging ROIs is allowed.

Segment tractogram into fiber categories

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

Freesurfer Deface

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca

Deprecated - Laplace Beltrami Spectrum

Lindsey Kitchell
This application will calculate the Laplace Beltrami spectrum of 3D surfaces in the .vtk file format using the LBS function provided with Mindboggle (http://www.mindboggle.info/). This application computes the Laplace-Beltrami spectrum using a linear finite element method, following the definitions and steps given in Reuter et al.'s 2009 paper: "Discrete Laplace-Beltrami Operators for Shape Analysis and Segmentation". Options for normalization are: None, "area", "index", "areaindex". Normalization by area uses the area of the 2D structure as...

WMC Figures (AFQ or WMA) - soichih

Soichi Hayashi
App to plot the fibers outputted from AFQ

Warp from subject space to MNI space

Daniel Bullock
This app warps your input set of ROIS to a reference space. As it is currently set up, the master branch of this app warps to MNI space.

FSL Brain Extraction (BET) on DWI

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

app-repeat-network-osg

Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

Cortex Tissue Mapping - DEPRECATED

Brad Caron
This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

pRFs / Benson14-Retinotopy

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

MBA plot tracts

Daniel Bullock
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Remove First B0 (temp)

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

TractSeg test

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

Knowing-what-you-know in brain segmentation

Nikhil Goyal
This App uses a pretrained deep neural network to predict FreeSurfer segmentations in minutes. The network was trained and evaluated on a large dataset (n = 11,148) obtained by combining data from more than a hundred sites. This App also produces the prediction uncertainty of the network at each voxel using two different uncertainty measures (entropy and variance). For more information please read https://arxiv.org/abs/1812.01719.

test

Brad Caron
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test

Brad Caron
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Anatomically-informed multi-LAP

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

Segment thalamic nuclei

Soichi Hayashi & Brad Caron
This app will segment the thalamus into its multiple components using the developer version of Freesurfer's segmentThalamicNuclei.sh function (http://freesurfer.net/fswiki/ThalamicNuclei). This app takes a Freesurfer segmentation in as an input and generates .mgz files with the appropriate thalamic segmentation inside the Freesurfer directory as an output.

Anatomically-informed multi-LAP with trk

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

Registration Year

  • 2019
    138

Resource Types

  • Software
    138