Hi Eugenio: As you advised, I ran the following command:
afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 Nicotine_HSF.txt Gathering results from subjects in: /Users/afrancis/Desktop/Connectome/HSF/ Using the suffix name: Smoke_e024 And writing them to: Nicotine_HSF.txt However, when I opened the Nicotine_HSF.txt, there was nothing there. The Subjects directory is the same folder. Please advice - thanks so much, Alan On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias <e.igles...@bcbl.eu> wrote: > Hi Alan, > the subfield module is not present in 5.3; you'll need to download the > development version (or wait until 6.0 is released, which should be pretty > soon=. > 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 > > ------------------------------ > *From: *"Alan Francis" <alandarkene...@gmail.com> > *To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, > "eiglesias" <eigles...@bcbl.eu> > *Sent: *Friday, December 11, 2015 6:36:42 PM > *Subject: *HSF in 5.3 > > Hi Eugenio: > I am trying to run the HSF method on 42 subjects. The FS version on our > cluster is 5.3. However when I use the following command I get an error > message. > > [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields > > ERROR: Flag -hippocampal-subfields unrecognized. > > -s Smoke_d004 -hippocampal-subfields > > Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 > x86_64 x86_64 x86_64 GNU/Linux > > > recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 > > > For more details, see the log file > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > I tried adding the -hippocampal-subfields-T1 but that did not work too. > > > thanks, > > > Alan > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > *Alan N. Francis PhD* > NIDA T32 Fellow in Computational Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> > afran...@mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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