Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters
Classifies streamlines into known anatomical tracts.
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
This app has been deprecated. It will only work with wmc_deprecated datatype.
This application converts Freesurfer's pial and white matter surfaces to different file types. It will convert the lh/rh.pial, lh/rh.white, lh/rh.smoothwm, lh/rh.inflated files into your choice of file type (stl, vtk, gii, mgz)
Index specific connections for a project
This application will reduce the number of vertices and faces on 3D surfaces by the percent reduction chosen.
Do some basic group analysis on freesurfer outputs
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).
Brainlife.io tutorial App
Pipeline for mouse brain skull-stripping and ROI segmentation
This application will calculate the Laplace Beltrami spectrum of 3D surfaces in the .vtk file format using the LBS function provided with Mindboggle (http://www.mindboggle.info/). This application computes the Laplace-Beltrami spectrum using a linear finite element method, following the definitions and steps given in Reuter et al.'s 2009 paper: "Discrete Laplace-Beltrami Operators for Shape Analysis and Segmentation". Options for normalization are: None, "area", "index", "areaindex". Normalization by area uses the area of the 2D structure as...
Service that does nothing (exist to do inter-resource transfer)
BIDS app for FS Tracula for BrainLife
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).
computes the volume of binary nifti images
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.
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm
Deterministic tracking using a peaks and metrics (PAM) (dipy_track_det)
This will give you the fiber count, mean length, standard deviation of length, total length, and volume of each fiber tract classified by AFQ or WMA.
Code to resample a tck file with a given step size.
Brain Extraction via FSL's BET command
This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.