Hi Floris
yes, taht is strange. We must have lost that option somewhere along the way. I think if you specify -3T it will set niterations to 1 (and also a couple of other things). We'll add it back in, but for no you could just edit the recon-all script to change nuiterations to be 1 by default (instead of 2)
sorry Bruce
On Fri, 25 Aug 2017, Floris van Vugt wrote:
Dear Freesurfer developers and community,
I am using recon-all as part of a pipeline and I am wondering about how to control the non-uniform intensity correction.
When I run `recon-all -help` I get:
-nuiterations
Number of iterations in the non-uniform intensity correction. Default is 1.
However, when I run `recon-all -i structural.nii -subjid foo -sd . -nuiterations 7` I get:
ERROR: Flag -nuiterations unrecognized. -nuiterations 7 Linux colossus 4.4.0-92-generic #115-Ubuntu SMP Thu Aug 10 09:04:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s exited with ERRORS at Wed Aug 23 15:27:55 EDT 2017
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I am running this version of Freesurfer:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Is this option deprecated? But then why is it still listed under freesurfer -help?
Thanks, Floris