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 ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu
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