Hi Barbara,
I'm not aware of any way that you can do it directly by passing arguments to recon-all (some might correct me on that), but it is possible:
1) As N3 models the bias as a multiplicative effect uncorrected = corrected * bias, the simplest way is to divide each voxel of the volume before and after correction, in order to obtain a volume containing the bias. Note that N3 (by default) works within a mask where low-intensity voxels have been thresholded away. These voxels will contain garbage if you divide all voxels in the volume.
2) Somewhat more complicated: you can specify the -keeptmp flag combined with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to preserve its working files. This requires you to modify the N3 binary call in the mri_nu_correct.mni script. You also need to convert the mnc files from the tmp dir, so that you can work with the volumes.
3) if you do 2), you also get hold of the low-intensity voxel mask that N3 operates within. You can use this to constrain the division mentioned in 1).
Best, Christian
On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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