1. Sigma is the smoothing kernel applied to the bias field so you can make
it pretty large depending on how high frequency your bias field is (typically
defined by the size of your receive coils)
2. min_dist specifies the minimum distance from the surface a voxel must be
for it to be considered as a potential control point
3. I don’t see why not although I’ve never tried it. It won’t fix
slice-specific artifacts in e.g. interlaced acquisitions
4. We estimate the bias field from the white matter, then apply it to the
whole brain.
I don’t think nonmax_suppress will do anything without surfaces though
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of James Brown
Sent: Tuesday, September 27, 2022 7:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter normalization of FLAIR images
External Email - Use Caution
Dear Dr Greeve and Dr Fiscle,
I am grateful to you guiding me through this. Indeed, I can see in
recon-all.log how Freesurfer 7.3.2 is normalizing the Flair images. it uses the
command below:
<mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg
aseg.presurf.mgz -surface lh.white identity.nofile -surface rh.white
identity.nofile FLAIR.prenorm.mgz FLAIR.norm.mgz >
I tried to run the previous command without the flag -surface" and it seems to
be working. using this command
<mri_normalize -seed 1234 -sigma 0.5 -nonmax_supress 0 -min_dist 1 --no-skull >
I would like to inquire about the following points and I highly appreciate any
clarification you might provide:
1- It seems mri_normalize uses default sigma of 8 for normalizing T1 images and
0.5 for Flair. How far can we go up with this value? More specifically, when I
have noticed when I increase sigma in noisy flair images in my dataset, I get
better out put images in terms of less noticeable motion artifacts. Is there
any cut off value for sigma? Can I use high values up to (e.g. 25)?
2- What does the flag "-min_dist" do? I tried to find information in
mri_normalize man (i.e. help ) but I couldn't find information about this flag.
I assume it has to do with the flag surface and they both should be used
together?
3- Can I use mri_normalize on 2D flair images ?
4- Is it recommended to do whole brain normalization (white/gray and csf) or
just white matter normalization within a mask.
Thank you very much for all that you do.
James
it looks like you are using v6. In v6, the flair might not have been normalized
On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote:
I think you need to add something like -FLAIRpial or -T2pial so it uses it (in
which case it will first normalize it), but hopefully someone else can confirm
cheers
Bruce
On Fri, Sep 23, 2022 at 2:40 PM James Brown
<jb1979...@gmail.com<mailto:jb1979...@gmail.com>> wrote:
Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the following
command line is reported in the "recon-all.log":
/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
FLAIR.nii.gz -s test
When I search for normalization of flair, I only find how Freesurfer normalized
T1.
I searched for "nonmax_suppress" and it is not in the log file. I am just
wondering what I am doing wrong. Thanks again for any highlights about the
correct method to normalize FLAIR
Sincerely,
Hi JamesB
there is T2/FLAIR normalization in recon-all if you process it through there.
You can look for "nonmax_suppress" if you want to find the command line
cheers
Bruce
On Fri, Sep 23, 2022 at 2:06 PM James Brown
<jb1979...@gmail.com<mailto:jb1979...@gmail.com>> wrote:
Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals and
experts in the field about the issue below.
Thank you for your kindness.
Dear Freesurfer experts,
In order to normalize white matter intensity of T1 images and correct for bias
field. We 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
We would like to apply bias field correction on FLAIR images then normalize
white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection we realize that the algorithm
has been developed to correct bias field correction in T1 not clear if it works
on FLAIR images.
Are the steps above valid for normalizing FLAIR images or can it only be
applied on T1 images? I would like to send a "recon-all.log" file that includes
the processing steps of FLAIR. Is there any link I can use to upload the file.
It gets rejected every time I send it due to size limitations.
We appreciate any feedback about the proper way to correct FLAIR images for
bias fields and normalize white matter intensity in FLAIR images.
Thank you
JamesB
On Wed, Sep 21, 2022 at 10:18 AM 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. We 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
We would like to apply bias field correction on FLAIR images then normalize
white matter intensity.
We tried N4biasfieldcorrection from ANTS but it didn't work as expected.
Reviewing documents about N4biasfieldcorrection we realize that the algorithm
has been developed to correct bias field correction in T1 not clear if it works
on FLAIR images.
Are the steps above valid for normalizing FLAIR images or can it only be
applied on T1 images? I would like to send a "recon-all.log" file that includes
the processing steps of FLAIR. Is there any link I can use to upload the file.
It gets rejected every time I send it due to size limitations.
We appreciate any feedback about the proper way to correct FLAIR images for
bias fields and normalize white matter intensity in FLAIR images.
Thank you
JamesB
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