External Email - Use Caution
What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Mikolas, Pavol" Pavol.Mikolas@uniklinikum-dresden.de Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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
That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Mikolas, Pavol" Pavol.Mikolas@uniklinikum-dresden.de Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
External Email - Use Caution
Dear Matthew,
thank you for this important point. I will check this. There might be just a few subjects with 8 and 32 head coil, so that it should be possible to discard them without affecting the sample size too much.
Do you think, you could give use some general hint to the ‘prescan normalize’ option? We cannot guess the benefit for our analysis well. Generally, if the benefit is rather low, we would tend to use the data without ‘prescan normalize’. What do you think?
Thank you, all best
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 15:44 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
External Email - Use Caution
Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil it isn’t so important to have on. It’s pretty much required for a 32CH coil, as the bias field is quite fast.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Mikolas, Pavol" Pavol.Mikolas@uniklinikum-dresden.de Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 17, 2020 at 9:02 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matthew,
thank you for this important point. I will check this. There might be just a few subjects with 8 and 32 head coil, so that it should be possible to discard them without affecting the sample size too much.
Do you think, you could give use some general hint to the ‘prescan normalize’ option? We cannot guess the benefit for our analysis well. Generally, if the benefit is rather low, we would tend to use the data without ‘prescan normalize’. What do you think?
Thank you, all best
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 15:44 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
________________________________ 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.
I would guess it is pretty important for a 12 channel also, although it depends on field strength and also needs a body coil transmit to be maximally effective. In general we use it whenever we can
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matthew Sent: Thursday, September 17, 2020 10:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil it isn’t so important to have on. It’s pretty much required for a 32CH coil, as the bias field is quite fast.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 9:02 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matthew,
thank you for this important point. I will check this. There might be just a few subjects with 8 and 32 head coil, so that it should be possible to discard them without affecting the sample size too much.
Do you think, you could give use some general hint to the ‘prescan normalize’ option? We cannot guess the benefit for our analysis well. Generally, if the benefit is rather low, we would tend to use the data without ‘prescan normalize’. What do you think?
Thank you, all best
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 15:44 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
________________________________ 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
Right I would recommend pre-scan normalize on for all images being acquired in a study. There are important considerations for fMRI, diffusion, and ASL (and even auxiliary scans like SE fieldmaps) not just T1w/T2w/FLAIR. That said, I was guessing that the FreeSurfer’s built in normalization could handle a 12CH receive field (based on my distant recollection of them) better than a 32CH receive field.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 17, 2020 at 9:39 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
I would guess it is pretty important for a 12 channel also, although it depends on field strength and also needs a body coil transmit to be maximally effective. In general we use it whenever we can
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matthew Sent: Thursday, September 17, 2020 10:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil it isn’t so important to have on. It’s pretty much required for a 32CH coil, as the bias field is quite fast.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 9:02 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matthew,
thank you for this important point. I will check this. There might be just a few subjects with 8 and 32 head coil, so that it should be possible to discard them without affecting the sample size too much.
Do you think, you could give use some general hint to the ‘prescan normalize’ option? We cannot guess the benefit for our analysis well. Generally, if the benefit is rather low, we would tend to use the data without ‘prescan normalize’. What do you think?
Thank you, all best
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 15:44 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
________________________________ 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.
External Email - Use Caution
Dear All, who answered,
thank you for your helpful hints. We will need to take a look at the data once more to see, where are the different coils and then decide using your advice.
All best
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 16:45 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Right I would recommend pre-scan normalize on for all images being acquired in a study. There are important considerations for fMRI, diffusion, and ASL (and even auxiliary scans like SE fieldmaps) not just T1w/T2w/FLAIR. That said, I was guessing that the FreeSurfer’s built in normalization could handle a 12CH receive field (based on my distant recollection of them) better than a 32CH receive field.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 9:39 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
I would guess it is pretty important for a 12 channel also, although it depends on field strength and also needs a body coil transmit to be maximally effective. In general we use it whenever we can
Cheers Bruce
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 Glasser, Matthew Sent: Thursday, September 17, 2020 10:15 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil it isn’t so important to have on. It’s pretty much required for a 32CH coil, as the bias field is quite fast.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 9:02 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matthew,
thank you for this important point. I will check this. There might be just a few subjects with 8 and 32 head coil, so that it should be possible to discard them without affecting the sample size too much.
Do you think, you could give use some general hint to the ‘prescan normalize’ option? We cannot guess the benefit for our analysis well. Generally, if the benefit is rather low, we would tend to use the data without ‘prescan normalize’. What do you think?
Thank you, all best
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 15:44 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
________________________________ 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.
I agree. The 8 channel coils can be trouble as they usually don’t have very good SNR at the vertex, so you are likely to see a lot of variance in the results in those regions
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matthew Sent: Thursday, September 17, 2020 9:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution That alone will be a huge factor in variable SNR (and receive field). Head coils are not interchangeable like that.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:22 AM To: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Matt,
unfortunately we have no highres T2w or FLAIR. In this multicentric study, we tended to use the 12 head coil. However, some centers used a 8 or a 32 head coil.
Thanks
Pavol
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Glasser, Matthew Gesendet: Donnerstag, 17. September 2020 14:14 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas@uniklinikum-dresden.demailto:Pavol.Mikolas@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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.
And more details about the study would also help. What field strength? Was the transmit coil a body coil? In the end though I’m not sure we are going to be able to give you an answer as it is an empirical question as to whether including them increases your variance more than it increases your power
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Glasser, Matthew Sent: Thursday, September 17, 2020 8:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR?
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Mikolas, Pavol" Pavol.Mikolas@uniklinikum-dresden.de Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer@nmr.mgh.harvard.edu'" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Prescan normalize and freesurfer
External Email - Use Caution Dear Freesurfer Developers,
I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options:
1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’
It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner.
Thank you, best regards
Pavol
________________________________ 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@nmr.mgh.harvard.edu
-
Fischl, Bruce -
Glasser, Matthew -
Mikolas, Pavol