FreeSurfer - aces/cbrain GitHub Wiki

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.

To run your analysis in CBRAIN, please follow the steps:

Please note the following prerequisites:

1. FreeSurfer licence file

To use the FreeSurfer tool and make it operational, you must first obtain a licence key. Obtaining the licence is free and comes in the form of a license.txt file. Once you have obtained the license.txt file, please upload it to CBRAIN and put the file in your system project.

Make sure the file is set to the type "FreeSurfer License". You only need to do this once.

Then you can launch Free Surfer by selecting the tool 'FreeSurferReconAll' and your NII input file, it will automatically use your license file too. Freesurfer (v7.4.1 most recent version) is available to all users.

You can download the licence key by clicking on this LINK.

2. Input format: Single NIfTI file

The FreeSurfer tool can only take one NIfTi file input at a time to run it successfully. If you want to select multiple NIfTI files and run FreeSurfer, then you will have to create a CBRAIN file list.

To create a CBRAIN File list, please:

• select the NIfTI files you want to run,
• click on the icon "More" in the right corner of the window,
• select "Create a file list" The file list will be created in your current project.

Process the Launch Task steps and select the FreeSurferReconAll tool, the server where you want to launch and the version:

• Select where you want to Save results to and to which Project
• Set up the task parameters according to your analysis.

Note:

• Any field marked with an * is mandatory.
• Remember, the FreeSurfer licence you saved in your system project will be automatically selected from there.

Then click on Start FreeSurferReconall

You can monitor the task by going to the task tab and checking on status:

You can navigate in the tree directory by expanding each folder and visualize files without the need to download them by simply clicking on the link. Once the image is loaded, you will be able to adjust settings such as the colour map or threshold, for example.

If you have any issues or questions, please don't hesitate to contact us @[email protected]