This app tracks between specified atlas regions to output a set of tracts.
converts wmc (output.mat) to trk files
repeat of fixed parameters for OHBM 2019 submission
app to calculate the Steklov Operator Spectrum on 3D surfaces
temp app to convert brainmask from dtiinit to mask datatype
computes the volume of binary nifti images
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)
This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.
Run freesurfer (v6) on Open Science Grid using fsurf command.
Estimate the quality of your diffusion-weighted data to map human connectomes.
Code to convert wmc to trk and resample with the given step size.
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.
ANTs transformation based on T1 and tractogram registration in MNI space
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
Service that does nothing (exist to do inter-resource transfer)
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).
Brainlife.io tutorial App
White matter bundle segmentation as Anatomically-Informed multiple Linear Assignment Problems (multi-LAP-anat).
This application checks and reports the orientation (neurological or radiological) of a nifti file.
Runs MRIQC pipeline (http://mriqc.readthedocs.io/en/stable/reports/smri.html) from Poldrack Lab on selected T1 anatomy.
This app will generate endpoint maps for all tracts in an input classification structure. User can specify what sort of decay/smoothing algorithm can be used (or none).
Hemodynamic Response Function Retrieval and Deconvolution (RS-HRF)
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