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Our group would be very interested in having this option available as well.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Tuesday, May 9, 2023 9:05 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] change ants N4 bias field correction parameter in
recon-all pipeline
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No, there is not an easy way to tweek the arguments to N4. I can add something
in dev. You can also hard code it by editing mri_nu_correct.mni (line 126)
On 5/9/2023 4:06 AM, 刘梦醒 wrote:
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Hello FreeSurfer Developers,
Some T1s we collected have higher intensity in the occipital cortex. The
default recon-all failed skull stripping and wm/gm segmentation in that part of
the brain. After several tests, we found that doing ants N4 bias field
correction with a shrink factor of 1 could fix the problem in most cases. We
are aware that the same correction is included in recon-all, while with default
parameters. We wonder if there is one way to specify the parameter for the bias
correction in recon-all?
If not, what would you recommend in this situation? A bias correction before
recon-all, and still do another correction inside recon-all?
The freesurfer we use is 7.1.1.
Thanks!
best,
Mengxing
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