140 Works

HCP Pipeline (FreeSurfer)

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.)

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.

Noddi Amico

Brad Caron
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs), and the single shell dwi file that has been aligned to the subject's T1 (i.e. dtiinit output) as input. The app will align the multi-shell data to the single-shell data...

Convert tck to trk in DWI space

Paolo Avesani
Convert a tractogram in tck format to a trk format file in dwi space

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.

Plot tract measures

Giulia Berto
Compute and plot total number of fibers, total number of nodes and average length of some tracts.

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.

Compute SNR on Corpus Callosum

David Hunt
Brainlife.io app that computes the signal-to-noise ratio in the corpus callosum

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...

Dipy Info

Soichi Hayashi, Serge Koudoro & Aman Arya
Provides useful information about different files used in medical imaging.

BIDS Mrtrix3 Connectome

Kate Alpert
BIDS app for Mrtrix3 Connectome DTI processing for BrainLife. Generates subject connectomes from raw image data using tools provided in the *MRtrix3* software package. http://www.mrtrix.org/. Optional preprocessing includes FSL's topup analysis for spatial correction and requires at least 2 input DTI images.

Tensor Mask

Soichi Hayashi, Serge Koudoro & Aman Arya
generate a mask from FA

Check T1 Orientation

Soichi Hayashi & Lindsey Kitchell
This application checks and reports the orientation (neurological or radiological) of a nifti file.

DP Fit Model with dtiInit

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

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

Noddi Amico (w/ dtiinit)

Brad Caron
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs), and the single shell dwi file that has been aligned to the subject's T1 (i.e. dtiinit output) as input. The app will align the multi-shell data to the single-shell data...

3D Tract Surfaces

Lindsey Kitchell
app to generate surfaces of each fiber tract

Convert trk to tck in T1 space

Soichi Hayashi & Paolo Avesani
Convert a tractogram in tck format to a trk format file in T1 space

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.

Non Local Means Denoising

Serge Koudoro
Applies nlmeans denoise (dipy / dipy_nlmeans)

Reconstruct Surfaces from LB Eigenfunctions

Lindsey Kitchell
This application will reconstruct the surfaces of each 3D model based on the selected number of eigenfunctions.

Test Gradient Flip for dtiInit processing

Soichi Hayashi & Lindsey Kitchell
This application will provide a recommendation on which axis you should flip the bvecs of your data, if it is necessary. It will perform fiber tracking using 4 different gradient flip options (no flip, x flip, y flip, and z flip) and report the most likely flip needed for your data. The flip recommendation is made based on the flip direction with the highest number of long fibers.

Registration Year

  • 2018
    140

Resource Types

  • Software
    140

Data Centers

  • Brainlife Production
    140