External Email - Use Caution

Hi Lilla,

Thank you for your quick response!

Infant freesurfer is only for use up to age 2, right?

I would be interested in trying the pipeline for older infants.

And also willing to discuss the lesion issue too.

Thank you!! Stef

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Monday, March 17, 2025 10:11 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology

You don't often get email from lzollei@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1QHz0vejszmx5Kj6r4Ul601cxmQg56xAqNuanZUrCBVxYISNhRTmOnvx011OtERPHG7mPiQ7tR27snyQx9IDb0jhhSBuZxxpZbNVXg3g9ZJdoZT18A5GySxCGbBc7m0LIA8P42XHIf8StHHkOQlYS4shYdoqjTaxAOsfxJmqp-3U4xjBseicaMpodscVJl2-HV3-dCRh008dAlQdsoYxiSGafIgL7dqk13GJixIqiwE0eF_tHzD_L4qYN3mgl70jOrVJEy2QqpRxgY6jQkrupzrvRcW4Z6f85mhFz69ckV3Q4u0Wo3bXzKWlFC6e6xnqE/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Hi Stef,

The infant FreeSurfer pipeline does rely on an infant training data set. What atlas did you have in mind?

At the moment, there is no way to include a lesion mask into the pipeline, but I would be happy to discuss that option.

Also, for your population, older infants, we have another pipeline you might want to try. Le me know whether you are interested,

Lilla

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Stefanie Bradley stefanie.bradley@mail.utoronto.ca Sent: Monday, March 17, 2025 9:53 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer Question - Pediatric pathology

External Email - Use Caution Hi there, I'm working with MRI scans from children aged 3-6 years old. I was wondering if there's a way to integrate pediatric atlases into the Freesurfer recon-all pipeline? I'm also wondering if it's possible to integrate a lesion mask into the pipeline in the case of brain pathology?

Thanks, Stef

STEFANIE BRADLEY

PHD CANDIDATE

Holland Bloorview Kids Rehab Hospital

150 Kilgour Rd, Toronto, ON M4G 1R8

stefanie.bradley@mail.utoronto.ca

[https://secure-web.cisco.com/1kWf2c8NzM8OclMTRcmltfW5rxRU9SRJI50sUcXDGlWqWxu...]https://secure-web.cisco.com/1uQzm_CoDmutDkOsJunQufG19PQx4c0AZhVnSO28l9XE9iJFgbLFNE4m44zUVLbnseTWcYFXMOCRSPe6QXEhiabARizKqJMSpXjzCJRAVhVwCKHqHi2LJ1GFpcqOJIFpPVexTxMV9HJeQxYIbfcgyUsu8s9lC40dxSGpte4ha3nF6m6gFchxAqG4z9s8K7SRftPNoRw1c7beHHvztalYiGBZFdDwEmNumrEOsokc_gzLcOnPMnxft0FAXank67zM7QSKUvYMchy_aDVZvDTOuXBZdIsp715yIajnURNu9FcyF4bmI5v2I_lRO53l0evKpbHF48jsIdctsazS1blWjxQ/https%3A%2F%2Fbme.utoronto.ca

Hi Stefanie, We have an in-house preschooler version of the script and for 4.5 / 5 yr-olds (depending on your data quality) you could also try to use the regular pipeline. We also wrote up a manual QC / editing guideline for 4-6 year-olds that you might want to look at: https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Stefanie Bradley stefanie.bradley@mail.utoronto.ca Sent: Wednesday, March 19, 2025 9:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology

External Email - Use Caution

Hi Lilla,

Just following up about this Freesurfer question. I've been using the NIH pediatric atlas for children aged 4.5-8 years old for parts of my analysis.

I'd be interested in hearing about the pipeline for older infants that you mentioned?

Thank you, Stefanie

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Stefanie Bradley stefanie.bradley@mail.utoronto.ca Sent: Monday, March 17, 2025 10:29 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology

You don't often get email from stefanie.bradley@mail.utoronto.ca. Learn why this is importanthttps://secure-web.cisco.com/1p74cs0NJIw4k-YM8myQlhgh8ss_g4NGXx92r2QkSpgOQwBMW7H5nqFYh2uWmZxWIU-HfHK4T5wm3Dhu5oLa_y2MCH_pmXlobvRQFeCJxirBoVxfMUluL4VV6j-Er3_2MzrgeFArUcNOto3_5QsWZkm4EW5pNag00o1A3MuyaVKLB6UcNB3J9Nyi4jPt1GGl-b65UaBIG-KKiPTuWLR7y49PCfB9s6rrkzhidne7FUwz2CzxTOusNTek5QCfQkMT_9USXb2q2aaPsdZtLOtFvyk2nz0mgg7zCI4fdm81fNR2qLNxtnWPrNrdRtkfLmOoD3L6uEA7KFy-zEal-uUDEtA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

External Email - Use Caution

Hi Lilla,

Thank you for your quick response!

Infant freesurfer is only for use up to age 2, right?

I would be interested in trying the pipeline for older infants.

And also willing to discuss the lesion issue too.

Thank you!! Stef

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Monday, March 17, 2025 10:11 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology

You don't often get email from lzollei@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1QHz0vejszmx5Kj6r4Ul601cxmQg56xAqNuanZUrCBVxYISNhRTmOnvx011OtERPHG7mPiQ7tR27snyQx9IDb0jhhSBuZxxpZbNVXg3g9ZJdoZT18A5GySxCGbBc7m0LIA8P42XHIf8StHHkOQlYS4shYdoqjTaxAOsfxJmqp-3U4xjBseicaMpodscVJl2-HV3-dCRh008dAlQdsoYxiSGafIgL7dqk13GJixIqiwE0eF_tHzD_L4qYN3mgl70jOrVJEy2QqpRxgY6jQkrupzrvRcW4Z6f85mhFz69ckV3Q4u0Wo3bXzKWlFC6e6xnqE/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Hi Stef,

The infant FreeSurfer pipeline does rely on an infant training data set. What atlas did you have in mind?

At the moment, there is no way to include a lesion mask into the pipeline, but I would be happy to discuss that option.

Also, for your population, older infants, we have another pipeline you might want to try. Le me know whether you are interested,

Lilla

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Stefanie Bradley stefanie.bradley@mail.utoronto.ca Sent: Monday, March 17, 2025 9:53 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer Question - Pediatric pathology

External Email - Use Caution Hi there, I'm working with MRI scans from children aged 3-6 years old. I was wondering if there's a way to integrate pediatric atlases into the Freesurfer recon-all pipeline? I'm also wondering if it's possible to integrate a lesion mask into the pipeline in the case of brain pathology?

Thanks, Stef

STEFANIE BRADLEY

PHD CANDIDATE

Holland Bloorview Kids Rehab Hospital

150 Kilgour Rd, Toronto, ON M4G 1R8

stefanie.bradley@mail.utoronto.ca

[https://secure-web.cisco.com/1kWf2c8NzM8OclMTRcmltfW5rxRU9SRJI50sUcXDGlWqWxu...]https://secure-web.cisco.com/1uQzm_CoDmutDkOsJunQufG19PQx4c0AZhVnSO28l9XE9iJFgbLFNE4m44zUVLbnseTWcYFXMOCRSPe6QXEhiabARizKqJMSpXjzCJRAVhVwCKHqHi2LJ1GFpcqOJIFpPVexTxMV9HJeQxYIbfcgyUsu8s9lC40dxSGpte4ha3nF6m6gFchxAqG4z9s8K7SRftPNoRw1c7beHHvztalYiGBZFdDwEmNumrEOsokc_gzLcOnPMnxft0FAXank67zM7QSKUvYMchy_aDVZvDTOuXBZdIsp715yIajnURNu9FcyF4bmI5v2I_lRO53l0evKpbHF48jsIdctsazS1blWjxQ/https%3A%2F%2Fbme.utoronto.ca