White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).
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.
Generate FA profiles
generate a mask from FA
This application checks and reports the orientation (neurological or radiological) of a nifti file.
A brain life app to prepare PRF and freesurfer data to be visualized with ui-3dsurfaces
Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.
This service cleans the output from AFQ and WMA using AFQ's AFQ_removeFiberOutliers function. For more information on the inputs of this application, please read the documentation at the top of the function: https://github.com/yeatmanlab/AFQ/blob/master/functions/AFQ_removeFiberOutliers.m
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...
app to generate surfaces of each fiber tract
Convert a tractogram in tck format to a trk format file in T1 space
This app takes in tracking data from the White Matter Segmentation app well as the nifti files of the user and gives tract profiles for each tracking file in a json format.
We present processed data from an investigation of the effects of long-term exposure to repetitive head impacts and brain tissue microstructure. Participants included 4th and 5th year varsity IU football players, 4th and 5th year varsity IU cross-country runners, and senior non-athlete IU students. We publish this dataset in hopes TBI researchers will be able to reproduce our results and perform new analyses to accelerate understanding.
Applies nlmeans denoise (dipy / dipy_nlmeans)
Generates connectome matrices and for T1 and BIDS datasets
Classifies streamlines into known anatomical tracts.
This application will reconstruct the surfaces of each 3D model based on the selected number of eigenfunctions.
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 ANTs transformation between two subjects based on T1 and FA volumes.
LiFE (Linear Fasicle Evaluation) predicts the measured diffusion signal using the orientation of the fascicles present in a connectome. LiFE uses the difference between the measured and predicted diffusion signals to measure prediction error. The connectome model prediction error is used to compute two metrics to evaluate the evidence supporting properties of the connectome.
Brainlife.io tutorial App
temp converter for raw datatype to noddi datatype