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