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:
External Email - Use Caution
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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