Hi Alan,
can you please list the files in the mri directory of any of the subjects and send me the output?
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: "Eugenio Iglesias" <e.iglesias@bcbl.eu>
Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, January 28, 2016 9:18:46 PM
Subject: Re: HSF in 5.3

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


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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
                                                                                                          
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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
                                                                                                          
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