FreeSurfer performs the whole cortical reconstruction process and generates it their unique FreeSurfer file format using the command recon-all. Outlined below are instructions on how to pre-process structural T1 data manually (which allows you to check and correct any errors), and automatically (which could encounter problems with segmentations and cortical tracing).
If you are interested in running longitudinal analysis, you will also need to pre-process the data using the longitudinal pre-processing pipeline.
Pre-processing with manual corrections
Ideally, you should run pre-processing with manual edits so you can check and correct any errors. If you do not wish to do this, you can run the whole pre-processing pipeline automatically (see next section below).
Run recon-all
This step simply creates an FTD### folder in your T1 folder and fills it with the files Freesurfer needs. Subsequent scripts will be run ONLY on this new folder, so you can delete the one in T1_Raw if you want at this point.
recon-all -i FTD####.nii -subjid subject_1
2. Run autorecon1
recon-all -subjid subject_1 -autorecon1
3. Run Tal Check. Open a terminal that allows GUI programs and run:
tkregister2 --mgz --s FTD### --fstal
This will open up the below tool box (and brain image). Use the buttons highlighted in green to move between views of the brain. Use the buttons highlighted in blue to switch between the actual brain and an averaged 'typical' brain. Confirm that the two brains match in terms of the angle of their tilt.
Figure A. Tal Check. Use the buttons highlighted in green and blue to check numerous points throughout the brain across the axes – comparing points on the actual (target) and mean (moveable) brain to identify any variation on the tilt. You do not need to check every slice.
4. If there is no variation between the actual and mean brain close the Tal Check window and run autorecon2.sh
recon-all -subjid subject_1 -autorecon2
Once this is finished, the scan is ready for manual edits.
If there is variation, the scan has failed the tal check. Consult with your supervisor. It is likely that this scan will not be used for processing.
5. Conduct manual editing and surface checks. Instruction on manual editing and surface checks on old FreeSurfer versions (v6.0 and below) can be found here. Official instructions on manual editing using new FreeSurfer versions (v7.0 and above) can be found here, and here.
6. Run QCACHE.sh. This is quite quick (about 20mins).
recon-all -subjid subject_1 -qcache
Running whole pre-processing pipeline automatically
You can automatically run the whole process (without manual editing/manual checks):
with a niftii file
recon-all -i FTD####.nii -subjid subject_1 -all
2. with a folder of DICOM files
recon-all -i /scratch/project/FTD#### -subjid subject_1 -all
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