thanks, i've fixed recon-all locally for the next release.

i added this line:

mkdir -p $subjdir/scripts

before this line:

set XOptsPreExist = $subjdir/scripts/expert-options

n.

On Fri, 2011-11-11 at 14:52 -0600, Michael Harms wrote:

Hi guys, There is an issue with recon-all abending if you use the -expert option on the very first call to recon-all, because recon-all attempts to copy to $subjid/scripts/expert-options before the scripts directory has been created.

As an attempted workaround I manually created an empty $subjid/scripts directory so that the directory already existed. However, in conjunction with the -i flag this then triggers the error of "existing subject" and the -force option no longer exists to force the process to proceed.

cheers, -MH

Ok, so a successful work-around strategy currently would be a two command approach:

recon-all -s $subjid -i input.nii recon-all -s $subjid -all -expert expert.opts

But it would be nice if recon-all -s $subjid -i input.nii -expert expert.opts

worked as well :)

cheers, -MH

On Fri, 2011-11-11 at 14:52 -0600, Michael Harms wrote:

Hi guys, There is an issue with recon-all abending if you use the -expert option on the very first call to recon-all, because recon-all attempts to copy to $subjid/scripts/expert-options before the scripts directory has been created.

As an attempted workaround I manually created an empty $subjid/scripts directory so that the directory already existed. However, in conjunction with the -i flag this then triggers the error of "existing subject" and the -force option no longer exists to force the process to proceed.

cheers, -MH