203 Works

Plot 3D Surfaces

Lindsey Kitchell
This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.

MRIQC

Soichi Hayashi
Runs MRIQC pipeline (http://mriqc.readthedocs.io/en/stable/reports/smri.html) from Poldrack Lab on selected T1 anatomy.

Connectome Evaluator (deprecated by app-life)

Soichi Hayashi
Estimate the quality of your diffusion-weighted data to map human connectomes.

Segment tracts between multiple brain regions from ROI directory

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of tracts.

Split Shells

Soichi Hayashi & Lindsey Kitchell
Split multi-shell diffusion data into a single chosen b value shell while rounding bvals

ROI Generation

Ilaria Sani & Brad Caron
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).

ANTs transformation and wmc registration with FA

Giulia Berto
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.

test

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

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Tract Analysis Profiles_deprecated

Brad Caron
This app has been deprecated. It will only work with wmc_deprecated datatype.

Vistasoft DWI T1 Registration

Brad Caron
This app will register a DWI image to a T1w image and rotate the bvecs. Requires a DWI image (with bvals and bvecs) and an T1w image (either ACPC-aligned or native). Will output an aligned DWI image, the rotated bvecs, and the bvals files.

White Matter Anatomy Segmentation

Daniel Bullock
Classifies streamlines into known anatomical tracts.

Freesurfer 6.0

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service allows you to submit T1 anatomical image and process it using Freesurfer, which is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. Please consider using OSG version to process a large number of subjects

AnalyzepRF on HCP data

David Hunt
An app to do a population receptive field analysis on HCP 7T retinotopy fMRI data

Ensemble Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell, Brent McPherson & Brad Caron
This service uses MRtrix 0.2.12 to do ensemble tracking using tensor and constrained spherical deconvolution (csd) algorithms. It generates a large set of candidate streamlines using a tensor-based deterministic model, csd-based deterministic model, and csd-based probabilistic model. The csd-based models can be computed at lmax values of 2, 4, 6, 8, 10, and 12. All candidate streamlines are combined into a single track.mat file. If you know the max lmax value for your data input...

LAP multiple examples without LiFE

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

Track between multiple brain regions from ROI directory

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) rois from an input directory to output a set of tracts.

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.

fMRI Preprocessing

Lollopasquini@Gmail.Com & Soichi Hayashi
fMRI preprocessing via CONN

helloworld

Soichi Hayashi & Franco Pestilli
Brainlife.io tutorial App

Registration Year

  • 2018
    140
  • 2019
    63

Resource Types

  • Software
    203

Data Centers

  • Brainlife Production
    203