Yes, I think so, but look through the recon-all.log file to confirm that it is using N3 and not N4 as I vaguely remember some issue that it would not run N3, but maybe I'm misremembering.

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Just want to confirm the following change is good to use to force use of ants-n3 with FS 7.2.

 

It appears as though FS 7.2 with ants-n3 gives us better results than the default n4.

We changed  /etc/recon-config.yaml to the following, and it appears to work and the recon-all log file appears to indicate N3 Nu intensity correction being used (see below). Is this change acceptable.

 

 

#--------------------------------------------

#@# Nu Intensity Correction Thu Sep 15 14:56:09 CDT 2022

 

mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n3

 

/usr/bin/bc

/data/shimony/shimony2/neonatal/freesurfer7_elabe_3yo/elabe_3yo_gdc_rdc_dn/MOD2532_Y3_a_fs7p2/mri

/usr/local/pkg/freesurfer7.2/bin/mri_nu_correct.mni

--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n3

nIters 2

mri_nu_correct.mni 7.2.0

Linux holowach 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Thu Sep 15 14:56:10 CDT 2022

tmpdir is ./tmp.mri_nu_correct.mni.43277

cd /data/shimony/shimony2/neonatal/freesurfer7_elabe_3yo/elabe_3yo_gdc_rdc_dn/MOD2532_Y3_a_fs7p2/mri

/opt/ANTs/bin/N3BiasFieldCorrection 3 orig.mgz ./tmp.mri_nu_correct.mni.43277/nu0.mgz

mri_binarize --i ./tmp.mri_nu_correct.mni.43277/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.43277/ones.mgz

 

7.2.0

 

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