Dear Freesurfer experts, I have noisy four MEMPRAGE images each one has four volumes for the same participant. These T1 images were acquired at the same scanning session. I have two question: 1. Is there any tool in free surfer to average these images. 2. Is the average the images a good idea to reduce noise and improve SNR 3. Do you suggest me any solution that can help to reconstruct these noisy images.
Thank you for any suggestion John
Hi John
sure, mri_average -rms will take the square root of the sum of squares of the 4 echoes if you want. You could then average them across the MEMPRAGEs if you want
cheers Bruce On Tue, 15 Aug 2017, John Anderson wrote:
Dear Freesurfer experts, I have noisy four MEMPRAGE images each one has four volumes for the same participant. These T1 images were acquired at the same scanning session. I have two question:
- Is there any tool in free surfer to average these images.
- Is the average the images a good idea to reduce noise and improve SNR
- Do you suggest me any solution that can help to reconstruct these noisy
images.
Thank you for any suggestion John
Dear Dr Bruce, Thank you very much for the quick response mri_average -rms will average the 4 volumes for each MEMPRAGE and output one T1 image. The results is four T1 images. How can I average these four T1 images. Can I merge them and use mri_average -rms gain?
-------- Original Message --------
Subject: Re: [Freesurfer] T1 motion and average Local Time: August 15, 2017 6:04 PM UTC Time: August 15, 2017 10:04 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
sure, mri_average -rms will take the square root of the sum of squares of the 4 echoes if you want. You could then average them across the MEMPRAGEs if you want
cheers Bruce On Tue, 15 Aug 2017, John Anderson wrote:
Dear Freesurfer experts, I have noisy four MEMPRAGE images each one has four volumes for the same participant. These T1 images were acquired at the same scanning session. I have two question:
- Is there any tool in free surfer to average these images.
- Is the average the images a good idea to reduce noise and improve SNR
- Do you suggest me any solution that can help to reconstruct these noisy
images.
Thank you for any suggestion John
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you wouldn't use -rms for the second round. That's a lot of averages though. Is your data quite hires? For 1mm or so we don't usually need more than a single scan at e.g. 3T and 32 channels. If your data is higher than 1mm, you should include the -noconform switch
cheers Bruce
On Tue, 15 Aug 2017, John Anderson wrote:
Dear Dr Bruce, Thank you very much for the quick response mri_average -rms will average the 4 volumes for each MEMPRAGE and output one T1 image. The results is four T1 images. How can I average these four T1 images. Can I merge them and use mri_average -rms gain?
-------- Original Message -------- Subject: Re: [Freesurfer] T1 motion and average Local Time: August 15, 2017 6:04 PM UTC Time: August 15, 2017 10:04 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
sure, mri_average -rms will take the square root of the sum of squares of the 4 echoes if you want. You could then average them across the MEMPRAGEs if you want
cheers Bruce On Tue, 15 Aug 2017, John Anderson wrote:
Dear Freesurfer experts, I have noisy four MEMPRAGE images each one has four volumes for the
same
participant. These T1 images were acquired at the same scanning
session. I
have two question:
- Is there any tool in free surfer to average these images.
- Is the average the images a good idea to reduce noise and improve
SNR
- Do you suggest me any solution that can help to reconstruct these
noisy
images.
Thank you for any suggestion John
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
John Anderson