Dear Bruce and Christian, I found the easy way of simply writing 'set cleanup = 0' at the beginning of mri_nu_correct.mni and then I run this command mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2
This way I get all the masks and iterations that were computed. Now I also see that it generates as many folders as there are iterations, ending with nu2_field and nu2_est if there are two iterations. I see more files now and now I am thinking that the last output is nu2_field, which would be the bias field. So this is why I did not divide anything by hand (also because my 001.mgz and the nu.mgz do not have the same image dimensions) and the info about masked-out voxel would be missing in that case. All the best and thanks. Barbara On 28/08/2014 14:46, Bruce Fischl wrote: > Hi Barbara > what exactly did you divide? If you look at the recon-all.log it will > show the exact inputs and outputs of nu_correct. > > cheers > Bruce > > > On Thu, 28 Aug 2014, Barbara Kreilkamp wrote: > >> 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 >> >> >> > _______________________________________________ > 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
