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Hi there,
My question is related to FreeSurfer’s calculations for intracranial volume (ICV): Given the importance to consider ICV as a potential covariate when assessing volumetric differences in ROIs between groups, which ICV output is recommended?
FreeSurfer’s recon-all generates eTIV (which is widely used by default in literature, and is a registration-based method). Conversely, the SAMSEG pipeline generates sbTIV (relatively newer approach which is a segmentation-based method). While these two would be the most obvious choice, many papers also consider correcting for supratentorial volume to be an appropriate approach.
To some degree, the choice of method would be guided by the research question. However in the most simple of cases (e.g., non-clinical cohorts), what method is recommended? Why would someone, for example, opt to use sbTIV over eTIV?
Warm regards, Jackson Lee
I’m not taking sides on this one, but I’ll nevertheless pinpoint that you can also get a sbTIV using SynthSeg, hehe. Looking forward to reading people’s opinions on this one!
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jackson Lee jacksonml@student.unimelb.edu.au Date: Tuesday, January 30, 2024 at 7:29 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Choice of ICV estimation
External Email - Use Caution Hi there,
My question is related to FreeSurfer’s calculations for intracranial volume (ICV): Given the importance to consider ICV as a potential covariate when assessing volumetric differences in ROIs between groups, which ICV output is recommended?
FreeSurfer’s recon-all generates eTIV (which is widely used by default in literature, and is a registration-based method). Conversely, the SAMSEG pipeline generates sbTIV (relatively newer approach which is a segmentation-based method). While these two would be the most obvious choice, many papers also consider correcting for supratentorial volume to be an appropriate approach.
To some degree, the choice of method would be guided by the research question. However in the most simple of cases (e.g., non-clinical cohorts), what method is recommended? Why would someone, for example, opt to use sbTIV over eTIV?
Warm regards, Jackson Lee
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Based on my personal experience, if you have T1 and T2 MRIs, use the sbTIV from samseg, and if you only have T1 MRI, use the TIV value from CAT12. Next, use the sbTIV from T1 samseg. I recommend not using the eTIV value for degenerative diseases.
Woo-Suk, Tae Seoul, Korea
2024년 1월 31일 (수) 오전 9:29, Jackson Lee jacksonml@student.unimelb.edu.au님이 작성:
External Email - Use CautionHi there,
My question is related to FreeSurfer’s calculations for intracranial volume (ICV): Given the importance to consider ICV as a potential covariate when assessing volumetric differences in ROIs between groups, which ICV output is recommended?
FreeSurfer’s recon-all generates eTIV (which is widely used by default in literature, and is a registration-based method). Conversely, the SAMSEG pipeline generates sbTIV (relatively newer approach which is a segmentation-based method). While these two would be the most obvious choice, many papers also consider correcting for supratentorial volume to be an appropriate approach.
To some degree, the choice of method would be guided by the research question. However in the most simple of cases (e.g., non-clinical cohorts), what method is recommended? Why would someone, for example, opt to use sbTIV over eTIV?
Warm regards,
Jackson Lee
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SX4ZEE_h46UB0tE8ncL1b8hMHcfiryNjOHvrdz_ECtYAJT... 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/1zG8aMF9AH3oSP5RVQWJofw5WrdOX3xINPlGSbjadwbM476... < https://secure-web.cisco.com/1zG8aMF9AH3oSP5RVQWJofw5WrdOX3xINPlGSbjadwbM476... .
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Thank you Woo-Suk and Juan for your emails,
For context, I have only T1 MRI scans. Would using volumes from recon-all and correcting these volumes for ICV using a different method (such as CAT12 as suggested) introduce some bias, as these measures are obtained from two different packages?
Jackson Lee
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Woo-Suk Tae woostae@gmail.com Date: Wednesday, 31 January 2024 at 11:37 am To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Choice of ICV estimation
External Email - Use Caution Based on my personal experience, if you have T1 and T2 MRIs, use the sbTIV from samseg, and if you only have T1 MRI, use the TIV value from CAT12. Next, use the sbTIV from T1 samseg. I recommend not using the eTIV value for degenerative diseases.
Woo-Suk, Tae Seoul, Korea
2024년 1월 31일 (수) 오전 9:29, Jackson Lee <jacksonml@student.unimelb.edu.aumailto:jacksonml@student.unimelb.edu.au>님이 작성:
External Email - Use Caution Hi there,
My question is related to FreeSurfer’s calculations for intracranial volume (ICV): Given the importance to consider ICV as a potential covariate when assessing volumetric differences in ROIs between groups, which ICV output is recommended?
FreeSurfer’s recon-all generates eTIV (which is widely used by default in literature, and is a registration-based method). Conversely, the SAMSEG pipeline generates sbTIV (relatively newer approach which is a segmentation-based method). While these two would be the most obvious choice, many papers also consider correcting for supratentorial volume to be an appropriate approach.
To some degree, the choice of method would be guided by the research question. However in the most simple of cases (e.g., non-clinical cohorts), what method is recommended? Why would someone, for example, opt to use sbTIV over eTIV?
Warm regards, Jackson Lee
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Iglesias Gonzalez, Juan E. -
Jackson Lee -
Woo-Suk Tae