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.
#--------------------------------------------
#@# 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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