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Brain Imaging and Behavior Lab

How to Load Files for FS Tasks

Quickchecks

These are just .png files, so you should be able to open them from File Explorer for PC or from Finder for Mac. Can be done on your computer or a lab computer.

Open Volumes and Surfaces from the Server in Freeview

These are .mgz files that are opened using Freeview. You must have FreeSurfer on your computer to view these files. For Mac, these are best opened via the Terminal.

On a lab computer:

  • Make sure you’ve first mounted the server
  • Open terminal
  • Navigate to /Volumes/CobiaResearch/project (‘cd /Volumes/CobiaResearch/project’)
  • Use ‘ls’ to list the contents, which is a list of all the current projects in the lab. Navigate to the project you are working on.
  • The .mgz file you want are located in a subject’s folder, which is usually found by going to ‘[project name]/PROCESSED_DATA/FREESURFER/[subject ID]
  • Within this subject folder, you can open the .mgz files you want with ‘freeview -v’, keeping in mind that they will probably be located within a sub directory. If I wanted to view the brainmask.mgz and aseg.mgz files for subject 3040_01_MR, for example, I would note that these files are in the ‘mri’ directory and execute the command:

freeview -v \

mri/brainmask/mgz \

mri/aseg.mgz:colormap=lut:opacity=0.4