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Aloha,
I am using Version 7.4.1. After running recon-all for multiple subjects, I noticed the Brain mask is larger than the intracranial volume (Mask-to-eTIV > 1). I attempted multiple different skull stripping methods, however, the mask-to-eTIV is always > 1. Any suggestions on how to fix this? Mahalo for your help.
Malama pono,
Krystalyn Edwards-Calma
This is not necessarily a problem. The "e" in eTIV means "estimate". It is a slight hack where the registration to MNI space is used to compute an estimate of the TIV, so it is not based on a segmentation or any real image processing, so it is sometimes quite off. This ratio was really just meant to be a flag to catch your attention. Now that it has it, just look at the skull stripping and see if it looks ok. If it does, then ignore the flag.
On 6/25/2025 6:49 PM, Krystalyn Edwards-Calma wrote:
External Email - Use CautionAloha,
I am using Version 7.4.1. After running recon-all for multiple subjects, I noticed the Brain mask is larger than the intracranial volume (Mask-to-eTIV > 1). I attempted multiple different skull stripping methods, however, the mask-to-eTIV is always > 1. Any suggestions on how to fix this? Mahalo for your help.
Malama pono,
Krystalyn Edwards-Calma _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
External Email - Use Caution
Aloha,
Mahalo for your response! What do you use for normalization between subjects?
Mālama Pono,
Krystalyn Edwards-Calma
On Jun 27, 2025, at 5:23 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This is not necessarily a problem. The "e" in eTIV means "estimate". It is a slight hack where the registration to MNI space is used to compute an estimate of the TIV, so it is not based on a segmentation or any real image processing, so it is sometimes quite off. This ratio was really just meant to be a flag to catch your attention. Now that it has it, just look at the skull stripping and see if it looks ok. If it does, then ignore the flag.
On 6/25/2025 6:49 PM, Krystalyn Edwards-Calma wrote: External Email - Use Caution
Aloha,
I am using Version 7.4.1. After running recon-all for multiple subjects, I noticed the Brain mask is larger than the intracranial volume (Mask-to-eTIV > 1). I attempted multiple different skull stripping methods, however, the mask-to-eTIV is always > 1. Any suggestions on how to fix this? Mahalo for your help.
Malama pono,
Krystalyn Edwards-Calma _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1MMb7ngXxdR7S6cxd8Jg9Q_yGYgnFj6FoyrmnMsABNPukkC...
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1MMb7ngXxdR7S6cxd8Jg9Q_yGYgnFj6FoyrmnMsABNPukkC... 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://secure-web.cisco.com/1LPuY3aaR5-wDJPPT3zpVdPPGYK3nwOAfGZ7j4L-4k20nPG... <https://secure-web.cisco.com/1LPuY3aaR5-wDJPPT3zpVdPPGYK3nwOAfGZ7j4L-4k20nPG... > . 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.
I would use the eTIV (or the sTIV in v8), but it is actually a philosophical question. If you normalize by the brain volume, you are testing a different hypothesis than if you normalize by the TIV.
On 6/27/2025 4:01 PM, Krystalyn Edwards-Calma wrote:
External Email - Use CautionAloha,
Mahalo for your response! What do you use for normalization between subjects?
Mālama Pono,
Krystalyn Edwards-Calma
On Jun 27, 2025, at 5:23 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
This is not necessarily a problem. The "e" in eTIV means "estimate". It is a slight hack where the registration to MNI space is used to compute an estimate of the TIV, so it is not based on a segmentation or any real image processing, so it is sometimes quite off. This ratio was really just meant to be a flag to catch your attention. Now that it has it, just look at the skull stripping and see if it looks ok. If it does, then ignore the flag.
On 6/25/2025 6:49 PM, Krystalyn Edwards-Calma wrote: External Email - Use Caution
Aloha,
I am using Version 7.4.1. After running recon-all for multiple subjects, I noticed the Brain mask is larger than the intracranial volume (Mask-to-eTIV > 1). I attempted multiple different skull stripping methods, however, the mask-to-eTIV is always > 1. Any suggestions on how to fix this? Mahalo for your help.
Malama pono,
Krystalyn Edwards-Calma _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1MMb7ngXxdR7S6cxd8Jg9Q_yGYgnFj6FoyrmnMsABNPukkC...
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1MMb7ngXxdR7S6cxd8Jg9Q_yGYgnFj6FoyrmnMsABNPukkC... 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://secure-web.cisco.com/1LPuY3aaR5-wDJPPT3zpVdPPGYK3nwOAfGZ7j4L-4k20nPG... <https://secure-web.cisco.com/1LPuY3aaR5-wDJPPT3zpVdPPGYK3nwOAfGZ7j4L-4k20nPG... > . 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.
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Krystalyn Edwards-Calma