Try looking at our tutorials on how to get started
http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials
but you can start by running
recon-all -s your-first-subject -i T1.nii.gz -all

On 12/21/2020 4:03 AM, 1248742467 wrote:

External Email - Use Caution

Hello, everyone

my freesurfer enviroment:

Last login: Mon Dec 21 16:45:53 2020 from 10.16.10.109

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME /home/tj/application/freesurfer

FSFAST_HOME /home/tj/application/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR /home/tj/application/freesurfer/subjects

cd /home/tj/application/freesurfer/subjects

MNI_DIR /home/tj/application/freesurfer/mni

I have a T1.nii.gz file, So where should I put this file in?

What's more, if I want to the output is in the input data file, how to set the recon-all command?
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