22 Works

Trekker - scalar testing

Soichi Hayashi, Franco Pestilli, , Brent McPherson & Brad Caron
Brainlife App (wrapper) for dMRI based fiber tracking using parallel transport tractography https://dmritrekker.github.io

app-mne-1

Julia Guiomar Niso Galan
Test

Network Plot Degree Distribution

Example template for network template using matlab

EFC identifiability

App on processing, analyzing eFC

Generate ROIs for Visual White Matter Tracking in dMRI Space (Glasser Parcellation) Binned by prf Eccentricity Estimates

Brad Caron
This app will generate ROIs that can be used for visual white matter tracking, including optic radiation tracking. This includes visual areas from the Glasser parcellation, the left and right LGNs from a thalamic nuclei segmentation, and exclusion ROIs from freesurfer. The ROIs will be resliced into diffusion space in of this. The Glasser ROIs will be binned by Eccentricity based on pRF mapping

app-test

Aurore Bussalb
test

Extract shell from DWI image

Brad Caron & Sophia Vinci-Booher
This app will extract diffusion gradient (i.e. shell) volumes from a DWI image using MrTrix3’s dwiextract function. Based on user input, will either include or exclude bzero volumes.

Compute myelin map using T1w / T2w ratio

Brad Caron
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Cortex Tissue Mapping (Native Space) - Myelin Mapping (T1w/T2w ratio)

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.

Multi-Atlas Transfer Tool

Soichi Hayashi, Josh Faskowitz, Franco Pestilli, Brent McPherson & Brad Caron
brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implementation of maTT2, which uses the gcs files trained on the mindboggle-101 data. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). Please consult the output parcellation key for the names of the nodes produced. These outputs are in the space of the T1w that was submitted to FreeSurfer's recon-all processes. In other words, the parc.nii.gz...

Parcellation Statistics - Surface

Brad Caron
This app will convert important parcellation statistics, including volume of each individual ROI given in a parcellation. These can be used for group analyses. This app should be used whenever possible to compute parcellation statistics (uses freesurfer's mri_annotation_stats).

HCP Pipelines - Structural preprocessing

Giulia Berto
brainlife wrapper for HCP Pipelines

app-maxfilter

Aurore Bussalb
Apply MaxFilter on MEG signals using MNE Python.

Compute summary statistics of diffusion measures mapped to cortical surface

Brad Caron
This app will This app will compute multiple summary statistics from measures mapped to the cortical midthickness surface on a per-ROI basis. This app takes in a cortexmap datatype and an optional parcellation/surface datatype. This app will compute the following summary statistics: minimum, maximum, mean, median, mode, standard deviation, sample standard deviation (n-1), and nonzero vertex count. The app will output a csv for each summary measure summarizing the diffusion measures in each ROI parcellation....

Network Degree Distribution

Template app to build new network neuroscience apps for brainlife

app-brainstorm_1_import_anatomy

Julia Guiomar Niso Galan
prueba

Fit qT1 models using mrQ

Brad Caron
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Cortex Tissue Mapping (Native & Template Space) - Myelin Mapping (T1w/T2w ratio)

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.

Matlab example

Example template for network template using matlab

Tract Analysis Profiles - Dipy

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

Network Aggregate

Example template for network analyses using matlab inside brainlife.

PyNets

Brad Caron, Derek Pisner, Franco Pestilli, Giulia Berto & Soichi Hayashi
A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

Registration Year

  • 2021
    22

Resource Types

  • Software
    22