Temporary app to remove first b0 for Athlete Brain Study Dataset
(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
This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.
This app segments tracts using pairs of (potentially multiple) rois from an input directory to output a set of tracts.
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...
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...
Classifies streamlines into known anatomical tracts.
Convert a tractogram in tck format to a trk format file in dwi space
This brainlife.io App will compute aggregrate statistics on the white matter tracts produced on brainlife.io. Statistics such as fiber count, tract volume, etc can be used to compare across tracts, across subjects either for scientific analyses or quality control of the results.
Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy
App to plot the fibers outputted from AFQ
Convert trk (trackvis) file to tck (mrtrix) format
This application checks and reports the orientation (neurological or radiological) of a nifti file.
Generate connection matrix for BIDS directories
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.
Generates connectome matrices and for T1 and BIDS datasets
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
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.
generate a mask from FA
Tesor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)
Fit a Diffusion Kurtosis Imaging model to multishell Diffusion-weighted data (dipy_fit_dki)