It all must be done. There is no tissue type segmentation per se. You can get it from the aseg.mgz The 3rd question is about FSL commands. you should contact FSL

On 12/5/2022 5:50 PM, Zeng, Qi wrote:

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Hi Freesurfer experts,

If I just want to normalize, register, and segment the T1-weighted images to the GM, WM, and CSF tissues, can certain steps be skipped from recon-all, such as the inflation process? What is the output for the segmentation of  GM, WM, and CSF tissues? is aseg.mgz or aparc+aseg.mgz better? Following that, if I want to apply an affine transformation for all subjects to a common template, is the following command line correct?

...

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz bet aparc+aseg.nii.gz my_structural.nii.gz flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in

my_structural.nii.gz -omat my_affine_transf.mat

...

fnirt --in=aparc+aseg.nii.gz --aff=my_affine_transf.mat

--cout=my_nonlinear_transf --config=T1_2_MNI152_2mm

...

applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm

--in=aparc+aseg.nii.gz --warp=my_nonlinear_transf --out=my_warped_structural

Best, QZ

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