138 Works

ROC curve (deprecated)

Soichi Hayashi & Giulia Berto
Plot ROC-AUC curve for multi-LAP and multi-NN. Warning: this app can be run ONLY after the app https://doi.org/10.25663/brainlife.app.174. This App was used specifically for a Reproducibility Study and has been deprecated.

Tract Analysis Profiles - Deprecated

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 (test)

David Hunt
runs fmriprep for brainlife

DWI Debias

Brad Caron
Performs mrtrix's dwibiascorrect on dwi data

Extract_files- copy

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Trekker ROI Tracking (parameters exposed)

Brad Caron
Brainlife App (wrapper) for dMRI based fiber tracking between ROIs using parallel transport tractography

STEM-IFOF: Segmentation of the Stem region of Inferior Fronto-Occipital Fasciculus

, Paolo Avesani & Pietro Astolfi
Automatic segmentation of the IFOF stem region (stem-ROI) using a Convolutional Neural Network (CNN). The dataset is composed of colored Fraction Anisotropy (cFA) images paired with the corresponding labeled stem-ROIs. In total there are 158 subjects, in which 128 have been used for training and 30 for test. For the test subjects the inferred stem-ROIs has been computed with the "TractSeg-BrainLife-test" app.

The human brain albinism and achiasma dataset: A biological testbed for the crossing-fibers problem with ground truth

Brent McPherson, Franco Pestilli & Robert Puzniak
Repository of T1- and diffusion-weighted magnetic resonance imaging data of individuals with albinism and achiasma.

Classifyber - segmentation

Giulia Berto
Code to run Classifyber as a pre-trained bundle segmentation method

fMRIPrep - Surface Output

Daniel Levitas, David Hunt, Josh Faskowitz & Soichi Hayashi
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

TractSeg

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
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

mrtrix3 act sift

Brent McPherson
test of adding sift as part of streamline generation to improve segmented anatomy quality

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.

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.

Associative white matter connecting the dorsal and ventral posterior human cortex

Franco Pestilli & Daniel Bullock
We present cortical endpoint termination data from a series of associative white matter tracts connecting the posterior human brain cortex. These tracts include the vertical occipital fasciculus (VOF), the posterior arcuate fasciculus (pArc), the temporo-parietal connection (TP-SPL), and the middle longitudinal fasciculus (MdLF).

app-repeat-tracking

Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

demo 1 ohbm

Franco Pestilli
hello

ROI Generation (no merge)

Brad Caron
Generate a parcellation volume (and roi nifti files split into each label) for specific ROIs, or every ROI, for a parcellation from freesurfer output and/or input parcellation volume. This App can also inflate input parcellation volume toward non-white matter voxels.

Bundle segmented tracks by eccentricity

Brad Caron, Franco Pestilli & Soichi Hayashi
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Prepare PRF output for visualization

Soichi Hayashi
A brain life app to prepare PRF and freesurfer data to be visualized with ui-3dsurfaces

AFQ Tract Classification

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
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...

ANTs tractogram registration in MNI space

Giulia Berto
ANTs transformation and tractogram registration in MNI space, using as the reference template the MNI152 T1 at 1.25 mm. WARNING: all the given inputs should be in the same anatomical space.

Convert Raw Noddi Datatype to Noddi Datatype

Brad Caron
temp converter for raw datatype to noddi datatype

ROI Generation (old)

Ilaria Sani & Brad Caron
Generate a parcellation volume (and roi nifti files split into each label) for specific ROIs, or every ROI, for a parcellation from freesurfer output and/or input parcellation volume. This App can also inflate input parcellation volume toward non-white matter voxels.

Registration Year

  • 2019
    138

Resource Types

  • Software
    138