124 Works

Network Matrices

Brent McPherson
create connectivity graphs from streamline tractography.

Compute SNR on Corpus Callosum

David Hunt
Brainlife.io app that computes the signal-to-noise ratio in the corpus callosum

LAP from 5 examples

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

ANTs transformation

Giulia Berto
Compute ANTs transformation between two subjects based on T1 and FA volumes.

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...

HCP ACPC Alignment (T2)

Soichi Hayashi, Brent McPherson & Brad Caron
This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.

Converts WMC to trk

David Hunt
converts wmc (output.mat) to trk files

Crop and Reorient T2

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

Recobundles

Serge Koudoro
Recobundles

HRSC: High Resolution Structural Connectome Processing

Kate Alpert
App for running high resolution structural connectome processing from Pierre Besson

DWI preproc and nonlinear registration to T1

Kate Alpert
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).

soichih/sca-service-noop

Soichi Hayashi
Service that does nothing (exist to do inter-resource transfer)

TractSeg HCP (test)

Lindsey Kitchell
Brainlife App for MIC-DKFZ/TractSeg. A tool for fast and accurate white matter bundle segmentation from Diffusion MRI using pretrained pytorch ML model.

3D Tract Surfaces

Lindsey Kitchell
app to generate surfaces of each fiber tract

Dorsal Attention Network

Brent McPherson
Index specific connections for a project

FreeSurfer Postprocessing

Brent McPherson
The converts labeled volumes to .nii.gz, creates white matter and corpus callosum masks, performs alignment to MNI space, and creates a 278 cortical labeled volume from Shen et al. 2013.

MRtrix2 Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service runs mrtrix 2.0 tracking spanning over multiple tracking methods and parameters (Probabilistic and Deterministic tracking). It generates three separate tracking outputs for each algorithm.

LiFE (dwi)

Soichi Hayashi, Martin Lindquist & Franco Pestilli
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.

Ensemble Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell, 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...

Connectome Evaluator (deprecated by app-life)

Soichi Hayashi
Estimate the quality of your diffusion-weighted data to map human connectomes.

mrtrix3 act

Brent McPherson
perform Anatomically Constrained Tractography (ACT) on single or multi-shell data.

Convert trk to tck

Soichi Hayashi
Convert trk (trackvis) file to tck (mrtrix) format

HCP ACPC Alignment (T1)

Soichi Hayashi, Brent McPherson & Brad Caron
This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.

Freesurfer Labels to 3D Surfaces

Lindsey Kitchell
This application will create a 3D surface for 87 freesurfer labels from the aparc+aseg.mgz file.

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

Resource Types

  • Software
    124

Publication Year

  • 2018
    87
  • 2017
    37

Registration Year

  • 2018
    124

Data Centers

  • Brainlife Production
    124