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Dear Dr Bruce, Fischl,
Indeed, the input to mri_segment is "brain.mgz", when I run mri_cnr on
brain.mgz I see
white = 102.3+-6.1, gray = 74.8+-16.7, csf = 51.5+-17.1

WM intensity is around 110  . I didn't know that intensity normalization
takes two steps! Thank you for pointing this out.


I would check your results to see if it is doing the right thing. I also
think that the input to mri_segment is not the norm.mgz, but rather the
brain.mgz, which is more aggressively normalized

On Mon, Oct 24, 2022 at 2:01 PM James Brown <jb1979...@gmail.com> wrote:

> Dear Dr Bruce, Fischl,
>
>
>
> The command was:
>
> mri_cnr $SUBJECTS_DIR/subjID/surf  $SUBJECTS_DIR/subjID/mri/norm.mgz
>
> I would like to understand the highest limit of WM intensity in a
> normalized image. I am a little bit confused about that. For instance, the
> command “mri_normlaize” puts white matter intensity around 110. It seems
> there is a high limit threshold for white matter (i.e. mri_segment puts wm
> high limit at 125 but in the manuscript I referenced it seems to be 140).
> If the image is showing higher intensity values due to a noise is it
> correct procedure to increase the high limit of WM up to 125 or 140?
>
>
> On Mon, Oct 24, 2022 at 1:46 PM James Brown <jb1979...@gmail.com> wrote:
>
>> Dear Dr Bruce, Fischl,
>>
>> Thank you very much for the detailed explanation. I would like to ask two
>> additional questions and I highly appreciate your input.
>>
>>
>>
>> -          The output of “mri_normalize” on a T1 image is something like:
>>
>>
>>
>> 3d normalization pass 1 of 2
>>
>> white matter peak found at 110
>>
>> white matter peak found at 109
>>
>> gm peak at 71 (71), valley at 38 (38)
>>
>> csf peak at 36, setting threshold to 59
>>
>> building Voronoi diagram...
>>
>>
>>
>> In this manuscript 
>> https://secure-web.cisco.com/1EhsES1ZezvIMDMxuS_URulqoaO_a1ha4QdRkq190T-vG90Ak4cg_CraqmjR8CUOtYb254N4k6pFa3b6Qi5g-MNzrqgnkFgGfoYbtwlO3XZmL_bi5ozDGEZmc_TyJbEG0wCGHLWBJPHxKZYlq26C29235IYTfatsx9a5WrZ_qtUO9G9OKnbzMqB0WVrBzE-E8kLexr19DdvYkXM1yoSuksq8Ufh2okemFrcBrQo-5gu4_A0zps-zNf4XVU0eX1irMeY_P9Ym0CIVRAIjRBCbokooOaR1abOR01Atpz12p-u3A93wtsK1OHbY-nPx4qQ27OO-iEIMCGDLagFJdmelJ5w/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F9931268%2F
>>  three
>> intensity-based contrasts WM_low (90), WM_high (140 and Gray_high (100)
>> were defined. I understand that the command “mri_normalzie” reports the
>> peak intensity of WM, GM and CSF but the highest limit of WM in any
>> “norm.mgz” is 140 by default. Is this correct?
>>
>>
>>
>> -          The output of the command “mri_cnr” is something like this:
>>
>> white = 86.5+-22.1, gray = 77.6+-29.0, csf = 66.8+-35.2
>>
>> lh CNR = 0.058
>>
>>
>>
>> Does this mean that the mean white matter intensity in the left
>> hemisphere is 86.5 and the standard deviation is 22.1? In this example, can
>> we say that the highest limit of white matter intensity in the image is 108?
>>
>>
>>
>> I apologize for asking too many questions. I appreciate the opportunity
>> to learn.
>>
>> Sincerely,
>>
>> James
>>
>>
>>
>>
>>
>> Hi James
>>
>>
>>
>> It really depends on your sequence. Some sequences, like mprage, trade
>> off SNR for CNR, so the distance between gray and white is larger, but the
>> noise in each is also larger. In that case white might end up brighter
>> because of the noise. There are also inflow effects where you get
>> non-inverted spins coming in through arteries that are very bright in
>> mprage, that you won’t see in a flash scan. We don’t actually set the gm
>> peak, just scale the white to 110-ish, then gray lands wherever the
>> intrinsic contrast of the image puts it
>>
>>
>>
>> Cheers
>>
>> Bruce
>>
>> On Sat, Oct 22, 2022 at 10:18 PM James Brown <jb1979...@gmail.com> wrote:
>>
>>> Dear Freesurfer experts,
>>> I would like to inquire about the flags "-whi" and "-ghi" in the
>>> command "mri_segement".
>>> According to FS wiki, the command "mri_normalize" sets white matter
>>> voxels around ~110 and gray matter around ~70.
>>> - The default white matter high limit in the command mri_segemnt is 125,
>>> what is the highest value to consider white matter voxels in an image? Is
>>> it 125?
>>> - What are the situations where we need to set the gray and white matter
>>> voxels at a high limit of 100 and 125 respectively in the command
>>> mri_segment? Does the brightness of the image or motion play a role in the
>>> decision of choosing high limits values?
>>>
>>>
>>> Thank you,
>>> James
>>>
>>
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