External Email - Use Caution
We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness in auditory cortex in Glasser and Van Essen 2011 Journal of Neuroscience). That said, at least in our hands we have had some issues with FreeSurfer 7.X and the hires stream. I’ve been hoping that the FS folks have a chance to investigate that soon, but for now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
In general, it’s good to have at least two voxels of grey matter for even the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1), which are about 1.6mm thick. This is where the HCP’s recommendation of at least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we didn’t stick with the typical 1mm resolution recommendation that was prevalent before the HCP).
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Lee, Sang Hoon" lsang2@med.miami.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, January 30, 2023 at 9:22 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] High resolution T1
External Email - Use Caution I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done. My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there any reference? Thank you so much for your time!
Sang H. Lee (Sr. Research Associate III) UM-Millier School of Medicine
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
Thank you so much for the information, Matt!
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matt Sent: Monday, January 30, 2023 1:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] High resolution T1
CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
External Email - Use Caution We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness in auditory cortex in Glasser and Van Essen 2011 Journal of Neuroscience). That said, at least in our hands we have had some issues with FreeSurfer 7.X and the hires stream. I’ve been hoping that the FS folks have a chance to investigate that soon, but for now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
In general, it’s good to have at least two voxels of grey matter for even the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1), which are about 1.6mm thick. This is where the HCP’s recommendation of at least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we didn’t stick with the typical 1mm resolution recommendation that was prevalent before the HCP).
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lee, Sang Hoon" <lsang2@med.miami.edumailto:lsang2@med.miami.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, January 30, 2023 at 9:22 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] High resolution T1
External Email - Use Caution I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done. My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there any reference? Thank you so much for your time!
Sang H. Lee (Sr. Research Associate III) UM-Millier School of Medicine
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
Dear, Matt,
What kind of issues did you have with version 7.x and the hires stream? It would help us to know what we are facing… Thanks.
Sang
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matt Sent: Monday, January 30, 2023 1:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] High resolution T1
CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
External Email - Use Caution We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness in auditory cortex in Glasser and Van Essen 2011 Journal of Neuroscience). That said, at least in our hands we have had some issues with FreeSurfer 7.X and the hires stream. I’ve been hoping that the FS folks have a chance to investigate that soon, but for now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
In general, it’s good to have at least two voxels of grey matter for even the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1), which are about 1.6mm thick. This is where the HCP’s recommendation of at least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we didn’t stick with the typical 1mm resolution recommendation that was prevalent before the HCP).
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lee, Sang Hoon" <lsang2@med.miami.edumailto:lsang2@med.miami.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, January 30, 2023 at 9:22 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] High resolution T1
External Email - Use Caution I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done. My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there any reference? Thank you so much for your time!
Sang H. Lee (Sr. Research Associate III) UM-Millier School of Medicine
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
On Mon, Jan 30, 2023 at 12:40 PM Lee, Sang Hoon lsang2@med.miami.edu wrote:
External Email - Use CautionDear, Matt,
What kind of issues did you have with version 7.x and the hires stream?
It would help us to know what we are facing…
Thanks.
Sang
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Glasser, Matt *Sent:* Monday, January 30, 2023 1:23 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [EXTERNAL] Re: [Freesurfer] High resolution T1
*CAUTION:* This email originated from outside the organization. *DO NOT CLICK ON LINKS* *or* *OPEN ATTACHMENTS* unless you know and trust the sender.
External Email - Use Caution *We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness in auditory cortex in Glasser and Van Essen 2011 Journal of Neuroscience). That said, at least in our hands we have had some issues with FreeSurfer 7.X and the hires stream. I’ve been hoping that the FS folks have a chance to investigate that soon, but for now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
In general, it’s good to have at least two voxels of grey matter for even the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1), which are about 1.6mm thick. This is where the HCP’s recommendation of at least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we didn’t stick with the typical 1mm resolution recommendation that was prevalent before the HCP).
Matt.
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Lee, Sang Hoon" lsang2@med.miami.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, January 30, 2023 at 9:22 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] High resolution T1
External Email - Use Caution *I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done.
My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there any reference?
Thank you so much for your time!
*Sang H. Lee* (Sr. Research Associate III)
UM-Millier School of Medicine
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/18vOJ6Mz_58dKWe49NnMQ1ikc1gn1wW_PjcqgFh0J6_SLs3... 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/1gl0MMFeytOpH46Zmu8hmVhALID701JslI1M8GZyAYppIk0... < https://secure-web.cisco.com/1gl0MMFeytOpH46Zmu8hmVhALID701JslI1M8GZyAYppIk0... .
External Email - Use Caution
Issues with surface placement in harder areas (e.g., white matter surface placement in heavily myelinated cortex; pial surface placement in lightly myelinated cortex).
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Lee, Sang Hoon" lsang2@med.miami.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, January 30, 2023 at 12:39 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] High resolution T1
External Email - Use Caution Dear, Matt,
What kind of issues did you have with version 7.x and the hires stream? It would help us to know what we are facing… Thanks.
Sang
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matt Sent: Monday, January 30, 2023 1:23 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] High resolution T1
CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
External Email - Use Caution We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness in auditory cortex in Glasser and Van Essen 2011 Journal of Neuroscience). That said, at least in our hands we have had some issues with FreeSurfer 7.X and the hires stream. I’ve been hoping that the FS folks have a chance to investigate that soon, but for now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
In general, it’s good to have at least two voxels of grey matter for even the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1), which are about 1.6mm thick. This is where the HCP’s recommendation of at least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we didn’t stick with the typical 1mm resolution recommendation that was prevalent before the HCP).
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lee, Sang Hoon" <lsang2@med.miami.edumailto:lsang2@med.miami.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, January 30, 2023 at 9:22 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] High resolution T1
External Email - Use Caution I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done. My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there any reference? Thank you so much for your time!
Sang H. Lee (Sr. Research Associate III) UM-Millier School of Medicine
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
In my experience, the issues that Matt is describing are mostly unique to the HCP data, but I have not tried it on much other hires data.
On 1/30/2023 1:54 PM, Glasser, Matt wrote:
External Email - Use Caution
Issues with surface placement in harder areas (e.g., white matter surface placement in heavily myelinated cortex; pial surface placement in lightly myelinated cortex).
Matt.
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Lee, Sang Hoon" lsang2@med.miami.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, January 30, 2023 at 12:39 PM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] High resolution T1
**
* External Email - Use Caution *
Dear, Matt,
What kind of issues did you have with version 7.x and the hires stream?
It would help us to know what we are facing…
Thanks.
Sang
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Glasser, Matt *Sent:* Monday, January 30, 2023 1:23 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [EXTERNAL] Re: [Freesurfer] High resolution T1
*CAUTION:*This email originated from outside the organization. *DO NOT CLICK ON LINKS* _or_ *OPEN ATTACHMENTS* unless you know and trust the sender.
* External Email - Use Caution *
We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness in auditory cortex in Glasser and Van Essen 2011 Journal of Neuroscience). That said, at least in our hands we have had some issues with FreeSurfer 7.X and the hires stream. I’ve been hoping that the FS folks have a chance to investigate that soon, but for now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
In general, it’s good to have at least two voxels of grey matter for even the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1), which are about 1.6mm thick. This is where the HCP’s recommendation of at least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we didn’t stick with the typical 1mm resolution recommendation that was prevalent before the HCP).
Matt.
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Lee, Sang Hoon" lsang2@med.miami.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, January 30, 2023 at 9:22 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] High resolution T1
**
* External Email - Use Caution *
I understand that from Version 7.0, better high resolution surface reconstruction with -hires is done.
My question is, if we use higher resolution T1, such as 0.8mm, will it improve the accuracy of the cortical thickness measurement? If yes, is there any reference?
Thank you so much for your time!
*Sang H. Lee* (Sr. Research Associate III)
UM-Millier School of Medicine
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Aaron Tanenbaum -
Douglas N. Greve -
Glasser, Matt -
Lee, Sang Hoon