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).
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 |
...
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 |
...