Brain Life

United States of America

41 Works

Convert Pial (Cortical) and White Matter Surfaces from Freesurfer

Lindsey Kitchell
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)

ROI Generation

Brad Caron
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).

Reconstruct Surfaces from LB Eigenfunctions

Lindsey Kitchell
This application will reconstruct the surfaces of each 3D model based on the selected number of eigenfunctions.

Noddi Amico

Brad Caron
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...

ROI to ROI Tracking

Ilaria Sani, Soichi Hayashi, Franco Pestilli & Brad Caron
This app will perform tracking between 2 cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. Inputs include: parcellation (freesurfer; atlas optional) with ROI niftis (generated from app-roiGeneration), dt6 from dtiinit, and ROI pairings. Outputs include a track.tck for each pairing of ROIs, a classification structure, and a fg_classified structure which can then be fed into other apps on the website (example: Clean WMC Output).

Ensemble Tracking

Lindsey Kitchell, Franco Pestilli, Brent McPherson & Brad Caron
This service uses MRtrix 0.2.12 to do ensemble tracking using tensor and constrained spherical deconvolution (csd) algorithms. It generates a large set of candidate streamlines using a tensor-based deterministic model, csd-based deterministic model, and csd-based probabilistic model. The csd-based models can be computed at lmax values of 2, 4, 6, 8, 10, and 12. All candidate streamlines are combined into a single track.mat file. If you know the max lmax value for your data input...

Compute Volume of Binary Nifti images

Soichi Hayashi & Lindsey Kitchell
computes the volume of binary nifti images

pRF

Justin Gardner, Soichi Hayashi, Franco Pestilli & Brad Caron
This app will compute a population receptive field (i.e. pRF) analysis on a given time series. Inputs needed include: a time series nifti, a stimulus nifti, the measurements of the visual stimulus in space (stimimageunits), and dimensions of a mask (mask; optional). Outputs include: x.nii, y.nii, rfWidth.nii and r2.nii. Please see http://gru.stanford.edu/doku.php/mrTools/tutorialsprf for more detail.

LAP single example without LiFE

Giulia Berto
Will run LAP_single example

LAP single example with LiFE

Giulia Berto & Brad Caron
Will run LAP_single example

Diffusion Predictor Grid Search (AppA) (master)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

ANTs transformation and wmc registration with FA

Giulia Berto
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.

ANTs transformation and wmc registration with T1

Giulia Berto
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.

Diffusion Predictor Grid Search (AppA)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

BHCK Tutorial

Lindsey Kitchell, Franco Pestilli & Brent McPherson
This app is an example for the brainhack 2018 tutorial. Should be deleted

Mutli-Atlas Transfer Tool

Brent McPherson & Brad Caron
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). Atlases include: gordon333, nspn500, yeo17, yeo17dil, hcp-mmp, schaefer100-yeo17, and schaefer-yeo17 (200, 400, 600, 800,...

Convert tck (MRtrix) files to trk (TrackVis) files

Soichi Hayashi & Lindsey Kitchell
This service will convert mrtrix tck files to tractvis trk files

Check dtiInit Orientation

Soichi Hayashi & Lindsey Kitchell
This application checks and reports the orientation (neurological or radiological) of a nifti file.

Check DWI Orientation

Soichi Hayashi & Lindsey Kitchell
This application checks and reports the orientation (neurological or radiological) of a nifti file.

Check T1 Orientation

Soichi Hayashi & Lindsey Kitchell
This application checks and reports the orientation (neurological or radiological) of a nifti file.

Test Gradient Flip

Soichi Hayashi & Lindsey Kitchell
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.

Split Shells

Soichi Hayashi & Lindsey Kitchell
This service will split multi-shell diffusion data into a single chosen b value shell. You need to run round-bvecs app before you run this app.

ACPC alignment via ART

Soichi Hayashi & Lindsey Kitchell
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.

Crop and Reorient T1

Soichi Hayashi & Lindsey Kitchell
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

Bias Field Correction

Soichi Hayashi & Lindsey Kitchell
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm

Resource Types

  • Software
    41

Publication Year

  • 2018
    25
  • 2017
    16

Registration Year

  • 2018
    41

Data Centers

  • Brainlife Production
    41