684 Works

Generate ROIs from pRF Eccentricity Estimates

Brad Caron
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Network Report

App to generate reports from networks. This includes network properties, node attributes and their respective distributions.

Justin Reslice T1w App

Justin Kilmarx
This is a template for a python-based brainlife.io/app

CIT168 parcellation of human subcortical brain nuclei

Daniel Bullock & Soichi Hayashi
A dockerized parcellation of human subcortical brain nuclei from the work of Pauli et al. 2018

Crop and Reorient T1

Soichi Hayashi & Brad Caron
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

Crop and Reorient T2

Soichi Hayashi, Brent McPherson & Brad Caron
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

Align mp2rage volumes to T1 using FSL Flirt

Brad Caron & Sophia Vinci-Booher
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Multi-Atlas Transfer Tool - old (w/surface output)

Soichi Hayashi, Josh Faskowitz, Franco Pestilli, Brent McPherson & Brad Caron
brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implemenation of maTT2, which uses the gcs files trained on the mindboggle-101 data. The GCS files are automatically pulled from the maTT fishare directory if not present locally. Inputs include: freesurfer, t1, atlas. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). These outputs are in the space of the T1w that was submitted to FreeSurfer's...

Matlab example

Example template for network template using matlab

Network Aggregate

Example template for network analyses using matlab inside brainlife.

Freesurfer

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis.

Mean amplitude of PSD data

Julia Guiomar Niso Galan
Compute the mean amplitude of a frequency range of PSD values

Mrtrix3 iFOD2 ROI Tracking (dwi)

Brad Caron
This app will generate multiple ROI to ROI tractograms using mrtrix3's probabilistic iFOD2 algorithm and anatomically constrained tractography framework (ACT).

LiFE - Multishell

Brent McPherson
This is a branch to the LiFE app that builds from my development fork

The Multi-Center Brain Glaucoma and Monocular Blindness Data Set

Franco Pestilli & Sandra Hanekamp
Using diffusion-weighted MRI and tractography, we investigated microstructural white matter (WM) alterations in thirty-seven human WM tracts in a total of 102 subjects, including subjects with glaucoma (GL), monocular blindness (MBL), and healthy controls (HC).

HCP Pipeline (PreFreeSurfer)

Brad Caron, Franco Pestilli, Giulia Berto, Kate Alpert & Soichi Hayashi
BIDS app for HCP pre-FreeSurfer for BrainLife. Performs ACPC alignment, FNIRT-based brain extraction, and bias field correction. (Please see https://github.com/Washington-University/HCPpipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#structural-preprocessing for more information on HCP structural pipelines.)

HCP Pipeline (FreeSurfer)

Brad Caron, Franco Pestilli, Giulia Berto & Kate Alpert
BIDS app for HCP FreeSurfer for BrainLife. Requires T1w_acpc_dc_restore.nii.gz, T1w_acpc_dc_restore_brain.nii.gz, and T2w_acpc_dc_restore.nii.gz from PreFS pipeline. (Please see https://github.com/Washington-University/HCPpipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#structural-preprocessing for more information on HCP structural pipelines.)

Brainstorm: MEG preprocessing

Julia Guiomar Niso Galan
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Generate images of DWI

Brad Caron
Create mid-axial, sagittal, and coronal slice png of DWI image

BROCCOLI (experimental)

Giulia Berto
Fast fMRI analysis on many-core CPUs and GPUs.

Tract Analysis Profiles (NODDI)

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

Extract diffusion metrics inside ROIs (DTI)

Brad Caron
This app will extracts diffusion metrics (tensor) from within ROIs for ROI-level analysis using FSL. Will output metric x ROI NIFTI images. Takes in DWI, tensor, NODDI, and ROIs inputs and outputs a directory with the metric x ROI NIFTI images. Inflation can be performed on the ROIs using SPM.

Extract diffusion metrics inside tissue types

Brad Caron
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Fit Tensor Model using MRTrix3

Brad Caron
This app will fit the diffusion tensor model (DTI) to a dMRI input using MRTrix3. The app can run on multi-shell or single shell data, and the user can specify which shell to use. This app can also normalize the diffusion data before model fitting based on user input. This app will output the neuro/tensor output on brainlife, including individual nifti files for FA, MD, AD, and RD, the tensors nifti, westin-shape niftis, and a...

[WIP] Create animation from trk

Soichi Hayashi
Generate animation of trk streamlines

Registration Year

  • 2022
    57
  • 2021
    144
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    683
  • Service
    1

Affiliations

  • The University of Texas at Austin
    4
  • Indiana University
    4