External Email - Use Caution

Thank you!

To resample a subject's surfaces to a common space (fsaverage), is the best way to use mri_surf2surf? E.g., for ?h.inflate, ?h.pial, etc.

And is using fsaverage appropriate to use for pediatric brains (aged 4-6 years old)?

Thanks, Stefanie

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, April 14, 2025 10:12 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

All outputs from recon-all are in native space

On 4/12/2025 5:57 PM, Stefanie Bradley wrote:

External Email - Use Caution

Hi there,

I wanted to clarify about the recon-all output: is it in the subject's native space or is everything already mapped to fsaverage space?

For example, is aparc.stats based on the brain in the subject's native space or has the cortical surface already been transformed to fsaverage space, and then stats (ex., cortical thickness) derived after that?

Thanks, Stefanie

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1kSG_iGk0V1o0AKjGB9mlGAgcLU0A1phxtQOAsTiIuzDBcR...

External Email - Use Caution

I'd like to be able to compare different subjects in a common space - would that require resampling to fsaverage?

Thanks, Stefanie ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, April 15, 2025 1:14 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

I'm not sure I know what you mean. Why do you want to map them to fsaverage? I'm cc'ing Lilla about the age question

On 4/14/2025 11:36 AM, Stefanie Bradley wrote:

External Email - Use Caution

Thank you!

To resample a subject's surfaces to a common space (fsaverage), is the best way to use mri_surf2surf? E.g., for ?h.inflate, ?h.pial, etc.

And is using fsaverage appropriate to use for pediatric brains (aged 4-6 years old)?

Thanks, Stefanie

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, April 14, 2025 10:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

All outputs from recon-all are in native space

On 4/12/2025 5:57 PM, Stefanie Bradley wrote:

External Email - Use Caution

Hi there,

I wanted to clarify about the recon-all output: is it in the subject's native space or is everything already mapped to fsaverage space?

For example, is aparc.stats based on the brain in the subject's native space or has the cortical surface already been transformed to fsaverage space, and then stats (ex., cortical thickness) derived after that?

Thanks, Stefanie

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10_Uej3F-z3Ttun-8AjpobdrzV1cw5I3P0T3mg03wuuU1pv...https://secure-web.cisco.com/1kSG_iGk0V1o0AKjGB9mlGAgcLU0A1phxtQOAsTiIuzDBcRnQkUoq1mO5i8ZfWBuYpJyn9WvNksGS1eqbWX850oo-X1B3uvPbZFcBo8FtH73z2ttjY9TNbye0p3ojW6eHlIC8sF-KOUfee18q0CBQDIwP_S3tdnvDf799y506KXyF7pT6oljTazQpbmdOUYFeqPlsnZ_Gm1lsF-IklUhb1xl0_rqXDnyvZjNnTCedtU8qoPbgd7mfxOG8gXTevqp5tEp7AQ-lNrPJ1CKHCQ-NvldWIK6fkGPwzWifEv1D5-tk1VzSWNERUDRYA_XN6PvN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/10_Uej3F-z3Ttun-8AjpobdrzV1cw5I3P0T3mg03wuuU1pv...

External Email - Use Caution

Ah yes, sorry: I'm interesting in comparing cortical thickness, total surface area, and gray matter volume.

And I was wondering about resampling the surfaces to fsaverag,e because I'd like to be able to visualize the inflated surface of each subject (in common space?) with overlays as well. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, April 15, 2025 1:51 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

But what are you comparing? Eg, thickness, or the white surface (somehow)?

On 4/15/2025 1:26 PM, Stefanie Bradley wrote:

External Email - Use Caution

I'd like to be able to compare different subjects in a common space - would that require resampling to fsaverage?

Thanks, Stefanie ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Tuesday, April 15, 2025 1:14 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

I'm not sure I know what you mean. Why do you want to map them to fsaverage? I'm cc'ing Lilla about the age question

On 4/14/2025 11:36 AM, Stefanie Bradley wrote:

External Email - Use Caution

Thank you!

To resample a subject's surfaces to a common space (fsaverage), is the best way to use mri_surf2surf? E.g., for ?h.inflate, ?h.pial, etc.

And is using fsaverage appropriate to use for pediatric brains (aged 4-6 years old)?

Thanks, Stefanie

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, April 14, 2025 10:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

All outputs from recon-all are in native space

On 4/12/2025 5:57 PM, Stefanie Bradley wrote:

External Email - Use Caution

Hi there,

I wanted to clarify about the recon-all output: is it in the subject's native space or is everything already mapped to fsaverage space?

For example, is aparc.stats based on the brain in the subject's native space or has the cortical surface already been transformed to fsaverage space, and then stats (ex., cortical thickness) derived after that?

Thanks, Stefanie

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attemp t from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1xuOV4OBpXBK6wkPjzJ7ukMuyTusvzSuqj0CpvkfM2yjAqd...https://secure-web.cisco.com/1kSG_iGk0V1o0AKjGB9mlGAgcLU0A1phxtQOAsTiIuzDBcRnQkUoq1mO5i8ZfWBuYpJyn9WvNksGS1eqbWX850oo-X1B3uvPbZFcBo8FtH73z2ttjY9TNbye0p3ojW6eHlIC8sF-KOUfee18q0CBQDIwP_S3tdnvDf799y506KXyF7pT6oljTazQpbmdOUYFeqPlsnZ_Gm1lsF-IklUhb1xl0_rqXDnyvZjNnTCedtU8qoPbgd7mfxOG8gXTevqp5tEp7AQ-lNrPJ1CKHCQ-NvldWIK6fkGPwzWifEv1D5-tk1VzSWNERUDRYA_XN6PvN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailSc anner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1xuOV4OBpXBK6wkPjzJ7ukMuyTusvzSuqj0CpvkfM2yjAqd...https://secure-web.cisco.com/10_Uej3F-z3Ttun-8AjpobdrzV1cw5I3P0T3mg03wuuU1pvu3ceSHPM-4_diiVv2UOK70d2zQ1sSEPkQSLeQjRT40wafRpBUlE2v7kH_ZSfe6Uuzr_cjHF1Ng3QPN3y1STzveQv66qtF9XJXAeZUayv39w2A6HEN9RXP0CHzJZIKylXfriJyqLgZ2vvVr5FgcrdQV5ttSC2eznjKOhxxlSzwNHCn1ONw-7_PSlJmZimYR-5fxcGvblOm79VIFzextjkNlmPow0iBxQjvk9WPkkU7QrgyqFLKMFVy669jVKRYgsAGSnrMDM0s13NVlpgYuUiE6Q1UFnQBYEmc1CvypYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1xuOV4OBpXBK6wkPjzJ7ukMuyTusvzSuqj0CpvkfM2yjAqd...

Yes, you should be able to use fsaverage for your age cohort. ________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, April 15, 2025 1:14 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

I'm not sure I know what you mean. Why do you want to map them to fsaverage? I'm cc'ing Lilla about the age question

On 4/14/2025 11:36 AM, Stefanie Bradley wrote:

External Email - Use Caution

Thank you!

To resample a subject's surfaces to a common space (fsaverage), is the best way to use mri_surf2surf? E.g., for ?h.inflate, ?h.pial, etc.

And is using fsaverage appropriate to use for pediatric brains (aged 4-6 years old)?

Thanks, Stefanie

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, April 14, 2025 10:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] clarification - recon-all output data

All outputs from recon-all are in native space

On 4/12/2025 5:57 PM, Stefanie Bradley wrote:

External Email - Use Caution

Hi there,

I wanted to clarify about the recon-all output: is it in the subject's native space or is everything already mapped to fsaverage space?

For example, is aparc.stats based on the brain in the subject's native space or has the cortical surface already been transformed to fsaverage space, and then stats (ex., cortical thickness) derived after that?

Thanks, Stefanie

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1kSG_iGk0V1o0AKjGB9mlGAgcLU0A1phxtQOAsTiIuzDBcRnQkUoq1mO5i8ZfWBuYpJyn9WvNksGS1eqbWX850oo-X1B3uvPbZFcBo8FtH73z2ttjY9TNbye0p3ojW6eHlIC8sF-KOUfee18q0CBQDIwP_S3tdnvDf799y506KXyF7pT6oljTazQpbmdOUYFeqPlsnZ_Gm1lsF-IklUhb1xl0_rqXDnyvZjNnTCedtU8qoPbgd7mfxOG8gXTevqp5tEp7AQ-lNrPJ1CKHCQ-NvldWIK6fkGPwzWifEv1D5-tk1VzSWNERUDRYA_XN6PvN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer