Create mid-axial, sagittal, and coronal slice png of T1 image with DWI outline overlayed
This app will merge two rois within an ROI datatype dataset into one ROI. The user must specify which two rois should be merged. The app will output one roi that contains all of the voxels that were in the two original rois.
This app will perform fsl_anat (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat)
We present diffusion and anatomical (T1w) processed data and derivatives from a group of IU athletes (football, cross-country) and non-athletes (students). The raw data contains both anatomical (T1 weighted) and diffusion-weighted (dMRI) magnetic resonance imaging data. The processed data shares 14 types of derivatives across 42 participants, comprising of 84 brainmasks (2 per participant), 42 Freesurfer outputs (1 per participant), 168 fiber orientation dispersion (FOD) images (4 per participant), 588 diffusion parameter maps (14 per...
This app will the individual tract tract profiles csv’s from the tractprofile dataype into a single summary csv for group analysis and machine learning. This app takes in a tractprofile datatype. The app will output a csv entitled ‘tracts.csv’ that can be used for group statistics and machine learning.
This app will generate optic radiations using MrTrix3's iFOD2 algorithm with the capability of using the Anatomically Constrained (ACT) framework
DSI Studio scripts converting DWI file to SRC format.
This is a little test of registering an app on Brainlife as part of the brain imaging course. This app takes an ACPC aligned anat/t1w data and resamples it to the desired resolution.
This App should be deleted. It used as an example for the class. The happy uses the code available at https://github.com/brainlife/app-template-python. The code is simple, it loads a t1w.nii.gz (which in brainlife.io is called neuro/anat) and resamples the file at the wanted resolution
This will fit the constrained spherical deconvolution model to an input DWI image. The outputs from this can be used for subsequent tracking apps.
This fits the NODDI model on single shell data. The only value that should be trusted is orientation dispersion (OD), as this measure can be fit accurately with single shell data
Improved version of the mrtrix3-preproc script deployed on BrainLife platform
Submit Freesurfer workflow on Open Science Grid (A national, distributed computing partnership for data-intensive research)
Convert a white matter classification (wmc) structure to a tractogram as a single trk file. Segmentation ID will be used to set bundle_code inside the .trk. You can access it with trk.tractogram.data_per_streamline["bundle_code"] with nibabel
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).
Generates an esemble of networks according to null models that try to reproduce the data. Erdos reyni (random), Barabási-Albert and Configuration model are implemented
Create mid-axial, sagittal, and coronal slice pngs of tensor outputs
This app will generate ROIs from a parcellation, subcortical structures found in the Freesurfer aseg, cortical structures found in the Freesurfer parcellations, and population receptive field visual area segmentations. The ROIs will be resliced into diffusion space in of this, merging ROIs is allowed.