Re: [Freesurfer] White matter normalization of FLAIR images

[Douglas N. Greve]

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  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:/



I tried to run the previous command without the flag -surface" and
it seems to be working. using this command



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 
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
 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 "r

Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

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  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:*
>
>  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
>
>  --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  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  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

Re: [Freesurfer] White matter normalization of FLAIR images

[Fischl, Bruce R.,PHD]

  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 
 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:



I tried to run the previous command without the flag -surface" and it seems to 
be working. using this command



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 
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 
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 
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_conver

Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

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:*



I tried to run the previous command without the flag -surface" and it seems
to be working. using this command



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  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  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  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 

Re: [Freesurfer] White matter normalization of FLAIR images

[Douglas N. Greve]

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

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of James Brown 


*Sent:* Friday, September 23, 2022 2:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] White matter normalization of FLAIR images

External Email - Use Caution

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  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 
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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Re: [Freesurfer] White matter normalization of FLAIR images

[Fischl, Bruce R.,PHD]

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of James Brown 

Sent: Friday, September 23, 2022 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] White matter normalization of FLAIR images


External Email - Use Caution

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 
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 
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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Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

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  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  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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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] White matter normalization of FLAIR images

[Fischl, Bruce R.,PHD]

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of James Brown 

Sent: Friday, September 23, 2022 2:06 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] White matter normalization of FLAIR images


External Email - Use Caution

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 
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] White matter normalization of FLAIR images

[James Brown]

External Email - Use Caution

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  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
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.