can you send your recon-all.log file?
On 9/15/2022 4:04 PM, James Brown wrote:
External Email - Use Caution
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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.
