Hello James,
I apologize that your message containing the log file got rejected. Can you
please re-send it? I will manually approve it so your conversation with Doug
can continue.
Liam Sennott
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of James Brown
<jb1979...@gmail.com>
Date: Friday, September 16, 2022 at 12:07 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] White matter normalization
External Email - Use Caution
I received the email below. any idea how I can send the recon-all log file to
Dr Greeve? Thank you
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Re: White matter normalization
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On Fri, Sep 16, 2022 at 10:25 AM James Brown
<jb1979...@gmail.com<mailto:jb1979...@gmail.com>> wrote:
Hi Dr Greeve,
I greatly apologize if I missed in the log file (attached) how freesurfer
normalizes flair. but I couldn't figure it out. Thanks for guidance
James
can you send your recon-all.log file?
On Thu, Sep 15, 2022 at 4:04 PM James Brown
<jb1979...@gmail.com<mailto:jb1979...@gmail.com>> wrote:
Hi Dr Greeve,
I ran recon-all using the flag -flair. I couldn't find any command in
recon-all.log that normalizes the flair images. It seems just normalization to
the T1.
I would like to inquire about the flag sigma in the command "mri_normalize" the
default is 8. when it is recommended to increase this value? and how much can
weincrease it?
I'm not sure of the order. You can run recon-all passing in the flair with
-flair flair.mgz. At some point in the process it will apply a normalization to
the flair (it will not necessarily be the same normalization that is applied to
the t1)
On Mon, Sep 12, 2022 at 4:01 PM James Brown
<jb1979...@gmail.com<mailto:jb1979...@gmail.com>> wrote:
Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for bias
field. I do the following steps:
mri_convert T1.nii.gz T1.mgz
mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2
mri_normalize -g 1 T1_N3.mgzT1_norm.mgz
mri_convert T1_norm.mgz T1_norm.nii.gz
I would like to apply bias field correction on FLAIR images then normalize
white matter intensity.
I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection I realize that the algorithm
has been developed to correct bias field correction in T1.
Are the steps above valid for FLAIR images or it can only be applied on T1
images. We appreciate any feedback about the proper way to correct FLAIR images
for bias field and normalize white matter intensity.
Thank you
JamesB
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