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)
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.
Brainlife.io tutorial App
Generate FA profiles
This service generates a csa model using dipy from a given dwi file and freesurfer mask. It then saves the evaluated peaks of the csa model into a dipy compatible .pam5 (peaks and models 5) file type for use in other dipy applications and scripts.
create connectivity graphs from streamline tractography.
A quality check application for tractography, segmentatations, and LiFE structures
Open Diffusion Data Derivatives (O3D). Reproducible Neuroimaging via open cloud services: Data upcycling to advance discovery in brain science
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).
Run HCP Pipeline powered by BIDS app
Takes a white matter classification resulting from a tract segmentation app and outputs one trk file for each segmented tract.
Fits a CSA model to diffusion data (dipy_fit_csa)
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm
app to generate surfaces of each fiber tract
This brainlife.io App implements the white matter segmentation of the vertical tracts described in Bullock et al. 2019. It segments 8 (4 per hemisphere) white matter tracts, the posterior Arcuate (pArc), temporal-parietal connection (TPC), middle-longitudinal fasciculus (MdLF-SPL MdLF-Ang) and the vertical occipital fasciculus (VOF).
This app is an example for the brainhack 2018 tutorial. Should be deleted
An app to do a population receptive field analysis on HCP 7T retinotopy fMRI data
Brain segmentation with the median_otsu method using DIPY. Default parameters work well on most volumes but you can play with them if needed
This app segments tracts using pairs of (potentially multiple) specified atlas regions to output a set of tracts.
App to plot the eigenfunctions of the Laplace Beltrami Spectrum.
This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.
Brain Extraction via FSL's BET command