Reconstruction Process

FreeSurfer Overview

Perform control point and white matter recon separately. Always start with control points, followed by white matter edits.
Don't edit white matter and then run control point recon, it will ignore your changes!
Reconstruction must all take place on the ba3 server.

CP Reconstruction
Once you have completed adding control points, go to the terminal to set your main subjects directory and add your job to the queue:

$ export SUBJECTS_DIR=/path/to/subjects/directory
$ echo "recon-all -autorecon2-cp -autorecon3 -subjid <Subject Folder Name>" | qsub -V -N <Subject Folder Name> -o ./logs/ -e ./logs/ -q recon

This will take ~10 hours. I recommend leaving it on the queue overnight.

WM Reconstruction
Then, complete white matter editing and run WM recon in the terminal:

$ export SUBJECTS_DIR=/path/to/subjects/directory
$ echo "recon-all -autorecon2-wm -autorecon3 -subjid <Subject Folder Name>" | qsub -V -N <Subject Folder Name> -o ./logs/ -e ./logs/ -q recon

This will also take ~10 hours.

Checking Your Status
Type in $ squeue -u <username> in the terminal.

• Make sure that the job is on the queue by ensuring that the S column says R, the job color is blue, and that the Time is elapsing. Your subject folder name will appear in the Name column.
• When it’s no longer on the queue, it means it’s done. Open up the brain on FreeView and review the changes made by your edits.

If there are issues, see Troubleshooting.

Next step: White Matter Edits or you're ready for final review!

FreeSurfer Overview