Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis.

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.

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.

Brain Extraction via FSL's BET command

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

Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca

This app will segment the thalamus into its multiple components using the developer version of Freesurfer's segmentThalamicNuclei.sh function (http://freesurfer.net/fswiki/ThalamicNuclei). This app takes a Freesurfer segmentation in as an input and generates .mgz files with the appropriate thalamic segmentation inside the Freesurfer directory as…

This small graphical user interface helps to map the anatomical borders of dentate gyrus in an imaged volume onto morphologies that had been reconstructed in that volume.

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.

Run freesurfer (v6) on Open Science Grid using fsurf command.

This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.

(We found an issue with this app. Please don't use) Align brains to the AC-PC plane by guessing their location given MNI coordinates

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