176 Works

Freesurfer Labels to 3D Surfaces

Lindsey Kitchell
This application will create a 3D surface for 87 freesurfer labels from the aparc+aseg.mgz file.

Fit MAPMRI

Soichi Hayashi, Serge Koudoro & Aman Arya
Fit MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng. Either the laplacian or positivity or both must be set to True. (dipy_fit_mapmri)

Diffusion Predictor Grid Search (AppA) (old)

Soichi Hayashi
This is an old version that used dwi instead of dtiinit

WMC Figures (AFQ or WMA) - soichih

Soichi Hayashi
App to plot the fibers outputted from AFQ

ANTs transformation and wmc registration with T1

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

Freesurfer on OSG

Soichi Hayashi & Lindsey Kitchell
Run freesurfer (v6) on Open Science Grid using fsurf command.

DP Fit Model with DWI

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.

Life reorient test

David Hunt
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Tract Profiles

Soichi Hayashi & Aman Arya
This app takes in tracking data from the White Matter Segmentation app well as the nifti files of the user and gives tract profiles for each tracking file in a json format.

app-fmri-2-mat

Soichi Hayashi & Josh Faskowitz
fmriprep outputs to connectivity matrices

app-run-fmriprep

Josh Faskowitz
runs fmriprep for brainlife

ACPC alignment via ART

Soichi Hayashi & Lindsey Kitchell
This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.

Connectome Mapper for BIDS datasets

David Hunt
Generates connectome matrices and for T1 and BIDS datasets

Warp from subject space to MNI space

Daniel Bullock
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DP Remove Tracts with DWI

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs Gen_niftis_remove_tracts

Peaks extraction

Giulia Berto
App to extract the peaks of a spherical harmonic function at each voxel.

Clean WMC output

Soichi Hayashi, Lindsey Kitchell & Daniel Bullock
This service cleans the output from AFQ and WMA using AFQ's AFQ_removeFiberOutliers function. For more information on the inputs of this application, please read the documentation at the top of the function: https://github.com/yeatmanlab/AFQ/blob/master/functions/AFQ_removeFiberOutliers.m

AFQ Tract Classification

Soichi Hayashi & Lindsey Kitchell
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...

AFQ Tract Classification with LiFE

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
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...

Network Neuro

Soichi Hayashi, Paolo Avesani, Franco Pestilli & Brent McPherson
Build structural brain networks using diffusion-weighted MRI, tractography and a brain atlas for cortical and subcortical parcellation.

LiFE with dtiInit

Soichi Hayashi, Paolo Avesani, Lindsey Kitchell & Franco Pestilli
LiFE (Linear Fasicle Evaluation) predicts the measured diffusion signal using the orientation of the fascicles present in a connectome. LiFE uses the difference between the measured and predicted diffusion signals to measure prediction error. The connectome model prediction error is used to compute two metrics to evaluate the evidence supporting properties of the connectome.

MRtrix2 Tracking with dtiInit

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service uses mrtrix 2.0 to track using three methods DTI-based Deterministic, CSD-based Probabilistic and Deterministic. It generates three separate tractograms (TCK), one for each algorithm.

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.

dtiInit

Soichi Hayashi, Paolo Avesani, Lindsey Kitchell & Franco Pestilli
Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1

Split Shells

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

Registration Year

  • 2018
    140
  • 2019
    36

Resource Types

  • Software
    169