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alhambrawebvr

WebVR test using photogrammetry models from the Alhambra in Granada, Spain.

app-3dfreesurfs

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

app-3dpialwm_freesurfer

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)

app-afq_figures

This service creates 4 figures of each AFQ tract: axial, left sagittal, right sagittal, coronal. Please choose the t1 image slices you would like displayed. The default slices work well for the HCP t1 images if they have not been re-ACPC aligned. If you have ACPC aligned your t1 images using the ACPC alignment app on Brain Life the following values are a good starting point: coronal = 105, sagittal = 89, axial = 65. The img_min and img_max values refer to the value range displayed for the t1 image. The value range is calulated as follow (mean + img_min * std, mean + img_max * std). The default values are a good starting place, adjust them if your t1 is too dark or too light.

app-afqclean

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

app-biasfieldcorrection

This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm

app-binvolvolume

computes the volume of binary nifti images

app-classifiedfibertractstats

This will give you the fiber count, mean length, standard deviation of length, total length, and volume of each fiber tract classified by AFQ or WMA.

app-convertsurfaces

convert file type of surface files

app-converttck2trk

This service will convert mrtrix tck files to tractvis trk files

app-crop_reorient_t1

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

app-decimatemesh

This application will reduce the number of vertices and faces on 3D surfaces by the percent reduction chosen. It can also be used to convert between filetypes.

app-deformetrica_register

register two objects using deformetrica

app-dipy-workflows

Brainlife wrapper app for Dipy workflows.

app-flipbvecs

app to flip the bvecs on one of the axes

app-generatetractmasks

app to generate binary masks of the segmented fiber tracts

app-generatetractsurfaces

app to generate surfaces of each fiber tract

app-lbscorrelationmatrices

code to create 2D matrices of the pearson correlation between the laplace beltrami spectrum of a group of subjects for each major tract from AFQ.

app-lbspectrum

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 in Reuter et al. 2006. Normalization by index will divide the eigenvalues by their index to account for linear increase of Eigenvalue magnitude (Weyl's law in 2D) as suggested in Reuter et al. (2006) and used in BrainPrint (Wachinger et al. 2015). The default is areaindex, which will do both. References (please cite when using for publication): Martin Reuter et al. Discrete Laplace-Beltrami Operators for Shape Analysis and Segmentation. Computers & Graphics 33(3):381-390, 2009 Martin Reuter et al. Laplace-Beltrami spectra as "Shape-DNA" of surfaces and solids. Computer-Aided Design 38(4):342-366, 2006

app-lbspectrum_matlab

Application to calculate the Laplace Beltrami Spectrum and Eigenvectors using Matlab.

app-mrtrix3-act

Anatomically Constrained Tractography (ACT) using either single- or multi-shell diffusion-weighted MRI data.

app-networkmatrices

more flexible network app

app-noddi-amico

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 (if dtiinit was used for tracking; otherwise single shell data is not necessary) in order to assure that NODDI outputs are in the same space as the tensor outputs for later analyses. Will output the five NODDI output files: FIT_ICVF_NEW, FIT_OD_NEW, FIT_ISOVF_NEW, FIT_dir, and config.pickle.

app-normalizebvals

app for brainlife to normalize the bvals

app-plot3dobjects

This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.

app-ploteigenfunctions

App to plot the eigenfunctions of the Laplace Beltrami Spectrum.

app-reconstructlbeigenfunction

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

app-splitshells

app-steklovspectrum

app to calculate the Steklov Operator Spectrum on 3D surfaces

app-testgradientflip

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.