A quality check application for tractography, segmentatations, and LiFE structures. For the whole brain tractogram, provides a number of statistics associated with average streamline characteristics (i.e. count, volume occupied, avg length, length distribution). Does the same for the positively weighted streamlines of an FE structure if input. If a classification structure is input, provides a number of macrostructural statistics like stream count, volume, avg length, whole brain count/volume proportion, etc).
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.
Tesor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)
Brainlife wrapper app for Dipy workflows.
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.
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 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).
Estimate the quality of your diffusion-weighted data to map human connectomes.
RecoBundles - Automatic extraction of brain pathways
Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided.
Computes n equally spaced offset surfaces between the white and pial surfaces with equal ratios between areas of successive surfaces, which samples the same layers in gyri and sulci.
Will take a dt6 and create tensor (FA,MD,AD,RD) and Westin Shape Indices (cl, cp, cs) nifti images from a dt6.mat structure.
A quality check application for tractography, segmentatations, and LiFE structures
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.
Runs MRIQC pipeline (http://mriqc.readthedocs.io/en/stable/reports/smri.html) from Poldrack Lab on selected T1 anatomy.
Will run LAP_single example
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.
Brain Extraction via FSL's BET command
To monitor app-stage
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 app segments tracts using pairs of (potentially multiple) rois from an input directory to output a set of tracts.
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).