Dear Christian, Thanks a bunch for this answer. I ran all the steps you mentioned (except for the one where I simply do uncorrected/corrected, as these images have different dimensions, it seems nu3 does more than just normalization of intensities, but also image cropping). Do you know anything about the image cropping?
I ended up with the output nu1_mask and nu1_est and I think the last one is the bias field, at least it looks very much like one :). Am I right? Thanks for your help, Barbara On 27/08/2014 22:53, Christian Thode Larsen wrote: > 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 >> >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > _______________________________________________ > 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
