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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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