Re: [Freesurfer] Help with V6
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 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_merki...@rush.edu<mailto:douglas_merki...@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<http://www.jeiglesias.com> www.bcbl.eu<http://www.bcbl.eu> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer<http://www.bcbl.eu/legal-disclaimer> - Original Message - From: Noah Markowitz <noahb.markow...@gmail.com<http://gmail.com>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<http://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<http://www.jeiglesias.com> > www.bcbl.eu<http://www.bcbl.eu> > > Legal disclaimer/Aviso legal/Lege-oharra: > www.bcbl.eu/legal-disclaimer<http://www.bcbl.eu/legal-disclaimer> > > > - Original Message - > From: "Noah Markowitz" <noahb.markow...@gmail.com<http://gmail.com>> > To: freesurfer@nmr.mgh.harvard.edu<mailto: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.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
Re: [Freesurfer] Help with V6
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with V6
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
