Dear FS experts, I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer: recon-all -autorecon1 -subjid <subjid> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My questions are 1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter? 2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)? 3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space? Thanks in advance for the help! Best Regards, Yi Li (PhD) Senior Computational Scientist Computational Sciences The Jackson Laboratory Farmington, CT 06032 Tel: 860-837-2156 --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
