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