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.
This application will provide a recommendation on which axis you should flip the bvecs of your data, if it is necessary. It will perform fiber tracking using 4 different gradient flip options (no flip, x flip, y flip, and z flip) and report the most likely flip needed for your data. The flip recommendation is made based on the flip direction with the highest number of long fibers.
Compute and plot total number of fibers, total number of nodes and average length of some tracts.
computes the volume of binary nifti images
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).
app to generate binary masks of the segmented fiber tracts
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).
Do some basic group analysis on freesurfer outputs
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
Classifies streamlines into known anatomical tracts.
brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implemenation of maTT2, which uses the gcs files trained on the mindboggle-101 data. The GCS files are automatically pulled from the maTT fishare directory if not present locally. Inputs include: freesurfer, t1, atlas. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). These outputs are in the space of the T1w that was submitted to FreeSurfer's...
This app will align DWI data to a DTIINIT DWI dataset in order to fit models that require multi-shell data to tracking
App to convert the old wmc-deprecated datatype to the new wmc datatype
This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.
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.
Brain Extraction via FSL's BET command
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs), and the single shell dwi file that has been aligned to the subject's T1 (i.e. dtiinit output) as input. The app will align the multi-shell data to the single-shell data...
converts wmc (output.mat) to trk files
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...
ANTs transformation based on T1 and tractogram registration in MNI space
Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca
Convert a tractogram in tck format to a trk format file in dwi space