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Yes, recon-all log file only indicates use of ants-N3, no use of N4. See sample attached.
Just want to confirm this procedure is correct.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 20, 2022 8:18 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] forcing use of ants-n3 with FS 7.2
* External Email - Caution * 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. On 9/16/2022 11:50 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution 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.
[cid:image001.png@01D8CCD7.4487B910]
#-------------------------------------------- #@# 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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