If you just want to normalize the flair, you can run samseg on it, ie,
samseg --i flair.mgz --o samseg.flair
in the output folder you will find a bias corrected volume
On 9/28/2022 7:42 AM, James Brown wrote:
External Email - Use Caution
Dear Dr Bruce,
Thank you very much for answering my questions and for help. We highly
appreciate you.
All the best
James
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
On Tue, Sep 27, 2022 at 7:20 AM James Brown <jb1979...@gmail.com> wrote:
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>
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> 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> 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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