This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of tracts.
This app segments tracts using pairs of (potentially multiple) specified atlas regions to output a set of tracts.
This app will perform tracking between 2 cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. Inputs include: parcellation (freesurfer; atlas optional) with ROI niftis (generated from app-roiGeneration), dt6 from dtiinit, and ROI pairings. Outputs include a track.tck for each pairing of ROIs, a classification structure, and a fg_classified structure which can then be fed into other apps on the website (example: Clean WMC Output).
Fits a CSA model to diffusion data (dipy_fit_csa)
Application to calculate the Laplace Beltrami Spectrum using matlab
This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.
Run freesurfer (v6) on Open Science Grid using fsurf command.
Open Diffusion Data Derivatives (O3D). Reproducible Neuroimaging via open cloud services: Data upcycling to advance discovery in brain science
Compute the Dice Similarity Coefficient (DSC) between corresponding tracts of the given segmentation and the ground truth when using HCP data.
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.
This service uses MRtrix 0.2.12 to do ensemble tracking using tensor and constrained spherical deconvolution (csd) algorithms. It generates a large set of candidate streamlines using a tensor-based deterministic model, csd-based deterministic model, and csd-based probabilistic model. The csd-based models can be computed at lmax values of 2, 4, 6, 8, 10, and 12. All candidate streamlines are combined into a single track.mat file. If you know the max lmax value for your data input...
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.
Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.
Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1
App for running mrtrix3 dwipreproc and then performing nonlinear registration of dwi to T1 (by running ANTs affine+nonlinear registration of CSF masks of mean b0 and T1). Bvectors are rotated with the affine transform. App is recommended for bringing dwi to T1 space if no phase encoding contrast between b=0 images was collected (so mrtrix3 dwipreproc cannot perform inhomogeneity field estimation).
This application will create a 3D surface for 87 freesurfer labels from the aparc+aseg.mgz file.
Code to resample a tck file with a given step size.
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.
Fit a CSD model to diffusion data (dipy_fit_csd)
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 reconstruct the surfaces of each 3D model based on the selected number of eigenfunctions.
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm with a single example. The user can specify up to eight tracts of interest, otherwise all the tracts of the given segmentation are considered as input.