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.edumailto: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.comhttp://www.jeiglesias.com www.bcbl.euhttp://www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimerhttp://www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: Noah Markowitz <noahb.markow...@gmail.comhttp://gmail.com> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.euhttp://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.comhttp://www.jeiglesias.com www.bcbl.euhttp://www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimerhttp://www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Noah Markowitz" <noahb.markow...@gmail.comhttp://gmail.com> To: freesurfer@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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