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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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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:
External Email - Use Caution
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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Our group would be very interested in having this option available as well. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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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External Email - Use Caution
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:
External Email - Use Caution
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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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Keefe, Sarah -
刘梦醒