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
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