Re: [Freesurfer] recon-all normalization: bias field output

Hi Barbara, Hang on, this will be slightly hairy. Right now, if you're not using the -3T flag when you run recon-all, you're essentially invoking N3 four times (the N3 wrapper, mri_nu_correct.mni). Every time you invoke N3, the output files are stored in separate directories (the once you located

Re: [Freesurfer] recon-all normalization: bias field output

Dear Freesurfers, The recon-all.log does not give info about the intermediate outputs (like nu2_est and nu2_field mnc-files), could you please confirm that the nu2_field.mnc is the bias field volume? It is the biggest file of all and is one of the last files generated by the script, but I would li

Re: [Freesurfer] recon-all normalization: bias field output

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 t

Re: [Freesurfer] recon-all normalization: bias field output

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

Re: [Freesurfer] recon-all normalization: bias field output

Hi Barbara, you should just be ble to divide the original image by the nu-corrected one to get the estimated bias field. cheers Bruce On Wed, 27 Aug 2014, Barbara Kreilkamp wrote: > Dear all, > > Is there a way to output the N3's (non-parametric normalization step) > output? > I am interested

Re: [Freesurfer] recon-all normalization: bias field output

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 anythin

Re: [Freesurfer] recon-all normalization: bias field output

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 bef