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 using recon-all automatically (which could encounter problems with segmentations and cortical tracing), and manually (which allows you to check and correct any errors), and automatically (which could encounter problems with segmentations and cortical tracing).
AFTER conducting recon-all:
If you are interested in running longitudinal analysis, you will also need to pre-process the data using the longitudinal pre-processing pipeline.
If you are interested in running analysis segmenting hippocampal subfields or amygdala, you should run further processing and analysis as outlined here.
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Running whole pre-processing pipeline automatically
You can automatically run the whole process (without manual editing/manual checks):
with a niftii file
| Code Block |
|---|
recon-all -i FTD####.nii -subjid subject_1 -all |
with a folder of DICOM files
| Code Block |
|---|
recon-all -i /scratch/project/FTD#### -subjid subject_1 -all |
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Pre-processing with manual corrections
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| Code Block |
|---|
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
| Code Block |
|---|
recon-all -i FTD####.nii -subjid subject_1 -all |
2. with a folder of DICOM files
| Code Block |
|---|
recon-all -i /scratch/project/FTD#### -subjid subject_1 -all |