Hello Noah,

Could you be more specific as to how you were able to resolve this problem? What additional tweaks were necessary? 

I too received the same error message:

ERROR: Flag -subfields-T1 unrecognized.
-all -s 1048_v6beta_hippsubfieldsT1 -subfields-T1
Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s xxxx exited with ERRORS at Fri Oct 23 13:10:17 CDT 2015 

I'm running freesurfer-Darwin-OSX-stable-v6-beta-20150921 on a mid 2012 MacPro (OS X 10.8.5). I also installed the Matlab runtime as instructed.

Any help would be greatly appreciated!

Thanks,

Doug

Doug Merkitch
Neurological Sciences
Rush University Medical Center
Email: Douglas_Merkitch@rush.edu



Thanks Noah. It doea say on the website that you need the 2012b runtime, but 
its definitely buried among too much other, less critical stuff
Cheers
E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


----- Original Message -----
From: Noah Markowitz <noahb.markow...@gmail.com>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST)
Subject: Re: [Freesurfer] Help with V6

Hey Eugenio,

I was able to resolve it with the help of another expert. One of the problems 
definitely was that 2014b doesn’t run on the hippocampal-subfields module. 
Maybe try adding that as a note to the website as numerous people have access 
to the 2014b version and 2015a was just released. Thanks again for all the help.

Cheers,
Noah

> On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias <e.igles...@bcbl.eu> wrote:
> 
> Hi Noah,
> this error is pretty weird. Can you please send us the exact command you 
> executed?
> Regarding the runtime: your 2014b runtime won't work. You need to follow the 
> instructions here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> 
> ----- Original Message -----
> From: "Noah Markowitz" <noahb.markow...@gmail.com>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, July 3, 2015 4:20:02 AM
> Subject: [Freesurfer] Help with V6
> 
> Hi,
> 
> I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the 
> error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and 
> source just as described for previous versions.
> 
> Also, I have Matlab 2014b downloaded on the computer (obviously comes with 
> runtime) but am unsure if the runtime folder needs to be placed in the FS 
> folder or is fine where it is. 
> 
> Any FS experts help with these two problems and concerns? Much appreciated if 
> you do.
> 
> Cheers,
> 
> Noah Markowitz
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