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.iglesias@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" <alandarkenergy@gmail.com>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, "eiglesias" <eiglesias@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
alanf@bwh.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
alanf@bwh.harvard.edu
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|