From: Michael Green <m.green@neura.edu.au>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, March 19, 2014 11:30 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] expert options command

I've been calling up an expert options file which contains the text "mri_normalize -gentle" but I'm having trouble executing it with this command:

"recon-all -s 002 -expert 002/scripts/expert.opts"

It results in the following error:

ERROR: there is a pre-existing expert options file and
you have specified an expert options file on the command-line.
If you want to use the file specified on the command-line,
you must run with -xopts-overwrite, or you may edit the
existing file /mridata/workingdata/INS/subjects/002/scripts/expert.opts (and not use the -expert option).

The help message is a little confusing (and not use the -expert option) but executing

"recon-all -s 002 -xopts-overwrite 002/scripts/expert.opts"

gives me the following error:

ERROR: Flag 002/scripts/expert.opts unrecognized.

Any ideas or help on this one?

--

Michael Green
Senior Research Officer
Lecturer, UNSW

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
T +61 2 9399 1086

neura.edu.au

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