Re: [Freesurfer] mri_normalize, 110 is too dark

[tvg[fs]]

Hi Bruce,

> You can't just change which peak is the WM - lots of things downstream would 
> fail

That is unfortunate.

I've send you the subject files and the raw files via filedrop (per
these instructions
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)


On Fri, Jul 29, 2016 at 4:38 PM, Bruce Fischl
 wrote:
> Hi Tom
>
> it's tough for us to tell without some images or the data. If you upload the
> entire subject dir of a subject that failed we will take a look. You can't
> just change which peak is the WM - lots of things downstream would fail
>
> cheers
> Bruce
>
>
>
> On Fri, 29 Jul 2016, tvg[fs] wrote:
>
>> Dear community and developers,
>>
>> I am experiencing issues during the normalization step, converting
>> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
>> and high intensity WM is ignored. The resulting T1.mgz collapses the
>> wrong voxels into the 110 bin.
>>
>> It seems that what mri_normalize assumes a peak in the WM intensity
>> distribution that is too low.
>> In NU.mgz WM seems centered around 140 not 110. Note that this is not
>> due to RF-field inhomogeneities. It is likely of physiological origin
>>
>> - Is there a way to explicitly tell mri_normalize to use a different
>> intensity peak?
>>
>> I realize that correction can be done with control points, however I
>> understand that does not compute a new intensity distribution, but
>> merely adds voxels around CPs. This is undesirable since I have >20
>> scans to process. Also this will not correct the falsely tagged GM
>> voxels.
>>
>> I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
>> (140-30 = 110). This did not give me the wished-for effect.
>> - Is it possible to bypass preprocessing steps of mri_normalize before
>> collapsing?
>>
>> - In general it would help if there is some elaboration on the options:
>> -no1d,
>> -nosnr,
>> -gentle,
>> -f vs -fonly,
>> -prune,
>> -g,
>> -monkey
>> - is [-monkey] just shorthand for [-no1d -n 1]?
>>
>> Thanks,
>> Tom
>>
>> System:
>> Mac OS X 10.10.5
>> freesurfer-Darwin-lion-stable-pub-v5.3.0
>>>
>>> mri_normalize --version
>>
>> stable5
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
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Re: [Freesurfer] mri_normalize, 110 is too dark

[Bruce Fischl]

Hi Tom

it's tough for us to tell without some images or the data. If you upload 
the entire subject dir of a subject that failed we will take a look. You 
can't just change which peak is the WM - lots of things downstream would 
fail

cheers
Bruce


On Fri, 29 Jul 2016, tvg[fs] wrote:

> Dear community and developers,
>
> I am experiencing issues during the normalization step, converting
> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
> and high intensity WM is ignored. The resulting T1.mgz collapses the
> wrong voxels into the 110 bin.
>
> It seems that what mri_normalize assumes a peak in the WM intensity
> distribution that is too low.
> In NU.mgz WM seems centered around 140 not 110. Note that this is not
> due to RF-field inhomogeneities. It is likely of physiological origin
>
> - Is there a way to explicitly tell mri_normalize to use a different
> intensity peak?
>
> I realize that correction can be done with control points, however I
> understand that does not compute a new intensity distribution, but
> merely adds voxels around CPs. This is undesirable since I have >20
> scans to process. Also this will not correct the falsely tagged GM
> voxels.
>
> I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
> (140-30 = 110). This did not give me the wished-for effect.
> - Is it possible to bypass preprocessing steps of mri_normalize before
> collapsing?
>
> - In general it would help if there is some elaboration on the options:
> -no1d,
> -nosnr,
> -gentle,
> -f vs -fonly,
> -prune,
> -g,
> -monkey
> - is [-monkey] just shorthand for [-no1d -n 1]?
>
> Thanks,
> Tom
>
> System:
> Mac OS X 10.10.5
> freesurfer-Darwin-lion-stable-pub-v5.3.0
>> mri_normalize --version
> stable5
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] mri_normalize, 110 is too dark

[tvg[fs]]

Dear community and developers,

I am experiencing issues during the normalization step, converting
NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
and high intensity WM is ignored. The resulting T1.mgz collapses the
wrong voxels into the 110 bin.

It seems that what mri_normalize assumes a peak in the WM intensity
distribution that is too low.
In NU.mgz WM seems centered around 140 not 110. Note that this is not
due to RF-field inhomogeneities. It is likely of physiological origin

- Is there a way to explicitly tell mri_normalize to use a different
intensity peak?

I realize that correction can be done with control points, however I
understand that does not compute a new intensity distribution, but
merely adds voxels around CPs. This is undesirable since I have >20
scans to process. Also this will not correct the falsely tagged GM
voxels.

I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
(140-30 = 110). This did not give me the wished-for effect.
- Is it possible to bypass preprocessing steps of mri_normalize before
collapsing?

- In general it would help if there is some elaboration on the options:
-no1d,
-nosnr,
-gentle,
-f vs -fonly,
-prune,
-g,
-monkey
- is [-monkey] just shorthand for [-no1d -n 1]?

Thanks,
Tom

System:
Mac OS X 10.10.5
freesurfer-Darwin-lion-stable-pub-v5.3.0
> mri_normalize --version
stable5
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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.