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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.