Dear all experts,
I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1".
Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log.
More info: ---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
---------------------------------------------------------------------
Dear Maximilià, first of all, sorry for the late response. We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it exists. If this is not the case in your system, maybe you could create an alias from 'mv' -> 'mv -f' before calling recon-all? 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
----- Original Message ----- From: "BAUTISTA-PERPINYA Maximilià" maximila.bautista-perpinya@etu.unistra.fr To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 18, 2016 9:35:05 AM Subject: [Freesurfer] Hippocampal subfields, stuck?
Dear all experts,
I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1".
Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log.
More info: ---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
---------------------------------------------------------------------
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
(+49) 015759302368 maximila.bautista-perpinya@etu.unistra.fr maxbauper@gmail.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Eugenio and all FS experts,
I tried your suggestion of making an alias 'mv' > 'mv -f', but it still didn't work. I am working on a tcsh shell. The alias does work when I type on the terminal, but doesn't seem to be changed when running recon-all. Any other suggestions? Any help could be greatly appreciated.
Best,
Max
On dijous 21 abril 2016 17:09 CEST, Eugenio Iglesias e.iglesias@bcbl.eu wrote:
Dear Maximilià, first of all, sorry for the late response. We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it exists. If this is not the case in your system, maybe you could create an alias from 'mv' -> 'mv -f' before calling recon-all? 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
----- Original Message ----- From: "BAUTISTA-PERPINYA Maximilià" maximila.bautista-perpinya@etu.unistra.fr To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 18, 2016 9:35:05 AM Subject: [Freesurfer] Hippocampal subfields, stuck?
Dear all experts,
I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1".
Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log.
More info:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
(+49) 015759302368 maximila.bautista-perpinya@etu.unistra.fr maxbauper@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
It worked! I was setting up the alias in the shell, and it didn't work. I set up now the alias as a global alias in the tcsh profile file (~/.tcshrc) and it worked. No problem this time.
Best,
MBP
On dijous 28 abril 2016 10:47 CEST, BAUTISTA-PERPINYA Maximiliàmaximila.bautista-perpinya@etu.unistra.fr wrote:
Hi Eugenio and all FS experts,
I tried your suggestion of making an alias 'mv' > 'mv -f', but it still didn't work. I am working on a tcsh shell. The alias does work when I type on the terminal, but doesn't seem to be changed when running recon-all. Any other suggestions? Any help could be greatly appreciated.
Best,
Max
On dijous 21 abril 2016 17:09 CEST, Eugenio Iglesias e.iglesias@bcbl.eu wrote:
Dear Maximilià, first of all, sorry for the late response. We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it exists. If this is not the case in your system, maybe you could create an alias from 'mv' -> 'mv -f' before calling recon-all? 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
----- Original Message ----- From: "BAUTISTA-PERPINYA Maximilià" maximila.bautista-perpinya@etu.unistra.fr To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 18, 2016 9:35:05 AM Subject: [Freesurfer] Hippocampal subfields, stuck?
Dear all experts,
I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1".
Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log.
More info:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
(+49) 015759302368 maximila.bautista-perpinya@etu.unistra.fr maxbauper@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg
(+49) 015759302368 maximila.bautista-perpinya@etu.unistra.fr maxbauper@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
BAUTISTA-PERPINYA Maximilià -
Eugenio Iglesias