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I received the email below. any idea how I can send the recon-all log file
to Dr Greeve? Thank you
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Re: White matter normalization
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On Fri, Sep 16, 2022 at 10:25 AM James Brown <jb1979...@gmail.com> wrote:
> Hi Dr Greeve,
> I greatly apologize if I missed in the log file (attached) how freesurfer
> normalizes flair. but I couldn't figure it out. Thanks for guidance
>
> James
>
>
>
> can you send your recon-all.log file?
>
>
>
>
> On Thu, Sep 15, 2022 at 4:04 PM James Brown <jb1979...@gmail.com> wrote:
>
>> Hi Dr Greeve,
>> I ran recon-all using the flag -flair. I couldn't find any command in
>> recon-all.log that normalizes the flair images. It seems just normalization
>> to the T1.
>> I would like to inquire about the flag sigma in the command
>> "mri_normalize" the default is 8. when it is recommended to increase this
>> value? and how much can weincrease it?
>>
>> I'm not sure of the order. You can run recon-all passing in the flair
>> with -flair flair.mgz. At some point in the process it will apply a
>> normalization to the flair (it will not necessarily be the same
>> normalization that is applied to the t1)
>>
>>
>>
>>
>> On Mon, Sep 12, 2022 at 4:01 PM James Brown <jb1979...@gmail.com> wrote:
>>
>>> Dear Freesurfer experts,
>>> In order to normalize white matter intensity of T1 images and correct
>>> for bias field. I 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
>>>
>>> I would like to apply bias field correction on FLAIR images then
>>> normalize white matter intensity.
>>> I tried N4biasfieldcorrection from ANTS but it didn't work as expected.
>>> Reviewing documents about N4biasfieldcorrection I realize that the
>>> algorithm has been developed to correct bias field correction in T1.
>>>
>>> Are the steps above valid for FLAIR images or it can only be applied on
>>> T1 images. We appreciate any feedback about the proper way to correct FLAIR
>>> images for bias field and normalize white matter intensity.
>>>
>>> Thank you
>>> JamesB
>>>
>>>
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