257 Works

ROI Generation (no merge)

Brad Caron
Generate a parcellation volume (and roi nifti files split into each label) for specific ROIs, or every ROI, for a parcellation from freesurfer output and/or input parcellation volume. This App can also inflate input parcellation volume toward non-white matter voxels.

pRFs / Benson14-Retinotopy

David Hunt
Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

Align HCP to Native Space

David Hunt
Aligns HCP fMRI data in MNI space to subject space

Peaks extraction

Giulia Berto
App to extract the peaks of a spherical harmonic function at each voxel.

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.

Align DWI to Dtiinit

Soichi Hayashi & Brad Caron
This app will align DWI data to a DTIINIT DWI dataset in order to fit models that require multi-shell data to tracking

pRFLife by Justin Gardner

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.

Remove First B0 (temp)

Brad Caron
Temporary app to remove first b0 for Athlete Brain Study Dataset

ROI Generation (thalamic nuclei)

Brad Caron
Generate a parcellation volume (and roi nifti files split into each label) for specific ROIs, or every ROI, for a parcellation from freesurfer output and/or input parcellation volume. This App can also inflate input parcellation volume toward non-white matter voxels.

Non Local Means Denoising

Serge Koudoro
Brainlife wrapper app for Dipy workflows.

Round b-values / Flip b-vecs for dtiInit

Soichi Hayashi & Lindsey Kitchell
(soon to be deprecated) This service round the b-values to the nearest 100. It will also flip the b-vecs around one or more chosen axes (please use Test Gradient Flip app to find out which one needs to be flipped). Some apps requires b-values to be round for their algorithms to work properly.

Segment tractogram into fiber categories

Soichi Hayashi
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).

Tractography quality check

Soichi Hayashi
A quality check application for tractography, segmentatations, and LiFE structures. For the whole brain tractogram, provides a number of statistics associated with average streamline characteristics (i.e. count, volume occupied, avg length, length distribution). Does the same for the positively weighted streamlines of an FE structure if input. If a classification structure is input, provides a number of macrostructural statistics like stream count, volume, avg length, whole brain count/volume proportion, etc).

Dipy Info

Soichi Hayashi, Serge Koudoro & Aman Arya
Provides useful information about different files used in medical imaging.

Test Gradient Flip for dtiInit processing

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.

Freesurfer

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis. Please consider using OSG version of Freesurfer (https://brainlife.io/app/5931c0b8ff090a00210eff09) to process a large number of subjects.

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.

Fit CSD

Soichi Hayashi, Serge Koudoro & Aman Arya
Fit a CSD model to diffusion data (dipy_fit_csd)

Clean WMC output

Soichi Hayashi, Lindsey Kitchell & Daniel Bullock
(deprecated by Remove Tract Outliers App) 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

Convert brainmask from dtiinit

Brad Caron
temp app to convert brainmask from dtiinit to mask datatype

Freesurfer Labels to 3D Surfaces

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

fMRIPrep

Daniel Levitas, David Hunt, Josh Faskowitz & Soichi Hayashi
runs fmriprep for brainlife

Registration Year

  • 2018
    140
  • 2019
    117

Resource Types

  • Software
    257