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2. Run autorecon1
| Code Block |
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recon-all -i FTD####.nii -subjid subject_1 -autorecon1 |
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4. If there is no variation between the actual and mean brain close the Tal Check window and run autorecon2.sh
| Code Block |
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recon-all -i FTD####.nii -subjid subject_1 -autorecon2 |
...
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).
| Code Block |
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recon-all -subjid subject_1 -qcache |
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Running whole pre-processing pipeline automatically
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