Hi Elisa,

Thanks for the update, does that mean that just adding -f to all rm in load_mgh.m worked for you? Sounds great, thanks for keeping us posted! Indeed, it's not that nobody computed the lGI, lots of people used it in published studies and from what I see in the mailing list, and I definitely used it on tons of different computer configurations, and only in one case I got this error message. It was on a lab unix server shared between many people where the rm command was aliased to copy files to the recycle bin. Not having access to this rm parameters, even using the rm -f didn't solve the problem. So, it's definitely not an lGI issue, but a rm issue…

Hope everything else will go well with your processing,

Marie


On Jul 3, 2014, at 2:59 AM, elisa veronese <dovreipensarci@gmail.com>
 wrote:

YEAH!
Now it is working, the '-f' option is doing something!
Actually it is still in progress, I do not know if it's going to work properly until the end. But at least something is happening :)

Thank you, Marie!
(Did you add the '-f' to all the rm in load_mgh.m?)

Best,

Elisa


2014-07-03 11:46 GMT+02:00 elisa veronese <dovreipensarci@gmail.com>:
Dear Marie,

thank fot your email. I'm quite confused, it seems like nobody has ever computed this localGI :(

Yes, before writing to the FS mailing list i checked in the internet if anybody had had my problem and I found your posts.
I will try adding the -f to force the removal, it could be an idea. I'll let you know.

Ehm... what do you mean by "to process the LGI on another computer"? Do you think it is a problem linked to the OS? 

Best,

Elisa


2014-07-02 19:17 GMT+02:00 Marie Schaer <Marie.Schaer@unige.ch>:


Hello Elisa,

I've seen this issue that the process gets stuck even if you answer the question. That happened to me and others before, see the following posts:



But I'm afraid that we didn't find the full solution to this yet. We tried replacing all the "rm" by "rm -f" in load_mgh.m, but it didnt help. Can you try that? Maybe you're more lucky than me. So finally, on my side, the only solution I found was to process the LGI on another computer… but it's definitely not ideal! 

Otherwise, maybe someone else has solved this issue without posting the reply on the mailing list. If yes, I'd be very grateful to know the answer, thanks in advance! 

Best,

Marie

On Jul 2, 2014, at 12:13 AM, elisa veronese <dovreipensarci@gmail.com>
 wrote:

Thank you Doug,

anyway I'm afraid I still have problems with the recon-all -localGI. After answering yes to the removal of the temporary file, it seems that the program stops without doing anything.
Now my tmp folder contains just one file (edit.dat). Below you can see what I see from my terminal. The terminal has been stuck there since yesterday.
Thank you.
Best
elisa

[root@gc02lx fselisa]# recon-all -s 1379341346/ -sd /root/Desktop/fselisa/ -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /root/Desktop/fselisa
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-r--r--. 1 root root 1658172 Jul  1 17:30 /root/Desktop/fselisa/1379341346/scripts/recon-all.log
Linux gc02lx 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /usr/local/freesurfer
    Previous: /home/tmp/6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer
/root/Desktop/fselisa/1379341346/surf
#--------------------------------------------
#@# Local Gyrification Index lh Tue Jul  1 17:31:13 CEST 2014

 mris_compute_lgi --i lh.pial

=================
rm -Rf /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.0000
=================
make_outer_surface('/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit
=================
Warning: Unable to open display 'iconic'.  You will not be able to display graphics on the screen.

                            < M A T L A B (R) >
                  Copyright 1984-2012 The MathWorks, Inc.
                    R2012b (8.0.0.783) 64-bit (glnxa64)
                              August 22, 2012

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
>> reading filled volume...
rm: remove regular file `/tmp/tp1773697773286350.load_mgh.2127429.mgh'? y




2014-06-27 20:25 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:

#1. not a problem
#2. yes, delete it

doug

On 06/27/2014 03:41 AM, elisa veronese wrote:
> Dear FS users,
>
> I'm trying the -localGI on a linux Centos machine, but I'm facing some
> problems:
> 1. should I worry about the /Warning: Unable to open display
> 'iconic'.  You will not be able to display graphics on the screen. /?/
> /
> 2. the script asks me if I wan to remove a file (rm: remove regular
> file `/tmp/tp726715349117711.load_mgh.8128471.mgh'?).  Should I say
> yes and remove it? Is it important? Should I keep it? I tried
> answering /no/, but now everything seems to be stuck without
> performing any subsequent processing.
>
> Below there is the output I got.
>
> Thank you.
> Regards,
> elisa
>
>
> [root@gc02lx fselisa]# recon-all -s 1379341346/ -sd
> /root/Desktop/fselisa/ -localGI
> INFO: FreeSurfer build stamps do not match
> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /root/Desktop/fselisa
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rw-r--r--. 1 root root 1624545 Jun 26 18:08
> /root/Desktop/fselisa/1379341346/scripts/recon-all.log
> Linux gc02lx 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT
> 2013 x86_64 x86_64 x86_64 GNU/Linux
> INFO: current FREESURFER_HOME does not match that of previous processing.
>     Current: /usr/local/freesurfer
>     Previous:
> /home/tmp/6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer
> <http://6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer>
> /root/Desktop/fselisa/1379341346/surf
> #--------------------------------------------
> #@# Local Gyrification Index lh Fri Jun 27 09:23:34 CEST 2014
>
>  mris_compute_lgi --i lh.pial
>
> =================
> rm -Rf /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial
> =================
> =================
> mkdir -p
> /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial
> =================
> =================
> mris_fill -c -r 1 lh.pial
> /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> =================
> reading surface from lh.pial...
> writing filled volume to
> /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
> conforming output volume
> setting resolution for intermediate calculations to 1.0000
> =================
> make_outer_surface('/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
> exit
> =================
> Warning: Unable to open display 'iconic'.  You will not be able to
> display graphics on the screen.
>
>                             < M A T L A B (R) >
>                   Copyright 1984-2012 The MathWorks, Inc.
>                     R2012b (8.0.0.783) 64-bit (glnxa64)
>                               August 22, 2012
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com
> <http://www.mathworks.com>.
>
> >> reading filled volume...
> rm: remove regular file `/tmp/tp726715349117711.load_mgh.8128471.mgh'?
>
>
>
> --
> Elisa Veronese - PhD
>
> /
> Research Unit on Brain Imaging and Neuropsychology (RUBIN)
> /
> /
> Inter-University Center for Behavioral Neurosciences (ICBN)
> University of Udine and University of Verona, Italy
> /
> ICBN Website: http://icbn.uniud.it/tiki-index.php
> /
>
> /
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
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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
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dispose of the e-mail.




--
Elisa Veronese - PhD

Research Unit on Brain Imaging and Neuropsychology (RUBIN)
Inter-University Center for Behavioral Neurosciences (ICBN)
University of Udine and University of Verona, Italy

_______________________________________________
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


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.




--
Elisa Veronese - PhD

Research Unit on Brain Imaging and Neuropsychology (RUBIN)
Inter-University Center for Behavioral Neurosciences (ICBN)
University of Udine and University of Verona, Italy




--
Elisa Veronese - PhD

Research Unit on Brain Imaging and Neuropsychology (RUBIN)
Inter-University Center for Behavioral Neurosciences (ICBN)
University of Udine and University of Verona, Italy