Sebastian,
Sorry for the oversight. The change to recon-all, as you have indicated, has been made to our source, and will appear in the next release.
Nick
On Tue, 2006-12-12 at 02:54 +0100, Sebastian Moeller wrote:
Hi Doug, hi list,
recently you implemented a version of mri_nu_correct.mni for me that allows for better settings for surface coil recordings. I dragged your change from 3.0.3 into 3.0.4 and just now realised, that it did not do anything ;), as the recon-all script in 3.0.4 does not process xopts for mri_nu_correct.mni. I guess in 3.0.3 I used the hacked version of nu_correct to hide the fact that recon-all dropped the xopts on the floor, oh my. Anyway recon-all of 3.0.4 only requires the following two edits: line 520 insert: set xopts = `fsr-getxopts mri_nu_correct.mni $XOptsFile`; and then replace the original line 521, now line 522 with the following: --o nu.mgz --n $NuIterations $xopts) (basically this adds "$xopts to the creation of cmd"). then it works like it expected.
Thanks for all the tools & the support Sebastian