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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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