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.
Fits a CSA model to diffusion data (dipy_fit_csa)
Brainlife.io tutorial App
Generate connection matrix for BIDS directories
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.
Temporary app to remove first b0 for Athlete Brain Study Dataset
SOCR KW wrapper for Brainlife
Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.
Classifies streamlines into known anatomical tracts.
This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.
Fit a CSD model to diffusion data (dipy_fit_csd)
fmriprep outputs to connectivity matrices
This service runs mrtrix 2.0 tracking spanning over multiple tracking methods and parameters (Probabilistic and Deterministic tracking). It generates three separate tracking outputs for each algorithm.
Tract Profile Output Aggregator
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.
Tesor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)
This app segments tracts using pairs of (potentially multiple) specified atlas regions to output a set of tracts.
(deprecated by Remove Tract Outliers App) 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
Performs ensemble tractography with MRTrix 0.2.12 with user specified values for lmax and curvatures across probabilistic, deterministic, and tensor methods. Additionally, it seeds and tracts extra streamlines through the corpus callosum.
Do some basic group analysis on freesurfer outputs
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.)
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm
Brain segmentation with the median_otsu method using DIPY. Default parameters work well on most volumes but you can play with them if needed
This application checks and reports the orientation (neurological or radiological) of a nifti file.
This app tracks between specified atlas regions to output a set of tracts.