date:20111230

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

2011-12-30 Thread James, Brian

Hi Ian,
Thanks for the information.  So I followed your instructions carefully with the 
same result (I modified the terminal options as well).  I also modified it as 
well to see if I can get it working but to no avail.  Here is the contents of 
my .tcshrc file:

#.tcshrc

# User specific aliases and functions

alias rm 'rm -i'
alias cp 'cp -i'
alias mv 'mv -i'
alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv 
SUBJECTS_DIR /usr/local/freesurfer/subjects; source 
$FREESURFER_HOME/SetUpFreeSurfer.csh'

set prompt='[%n@%m %c]# '

setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
source $FREESURFER_HOME/SetUpFreeSurfer.csh

Here is what my terminal looks like: Which looks correct to me

 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
[root@brian-Latitude-E6410 ~]# tkmedit bert config.mgz
/usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not 
executable.




From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ian Charest 
[ian.char...@mrc-cbu.cam.ac.uk]
Sent: December-30-11 7:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Brian

I had to change the terminal config for it to use tcsh.

I think Ubuntu now uses The Debian Almquist shell (dash) and I have had 
problems running freesurfer from it.

install tcsh using aptitude and then in the preferences of your terminal (Edit 
> profile preferences) in the tab "title and command" click on "run custom 
command instead of my shell" and type /bin/tcsh as your custom command.

You can also set up some environment variables by editing the .tcshrc found in 
your home directory.

>gedit ~/.tcshrc

and add a modified version of this code according to where your freesurfer 
install is and where your subject directory lies...

alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv 
SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'

now if you close your terminal and open a new one, freesurfer should work.

Hope it helps

Ian


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of James, Brian 
[brian.ja...@nbrhc.on.ca]
Sent: 30 December 2011 20:40
To: martijnsteenw...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

That is what I did…my path is /usr/local/freesurfer

However, mine doesn’t seem to work.


Brian.


From: Martijn Steenwijk [mailto:martijnsteenw...@gmail.com]
Sent: December-30-11 2:37 PM
To: James, Brian
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10


Just untarring the .tar.gz in /usr/local like documented here 
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on 
Ubuntu 11.10.

Best,
Martijn


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens James, Brian
Verzonden: vrijdag 30 december 2011 21:13
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Everyone,
I thought I would try installing FreeSurfer on Ubuntu because I 
was having so many issues trying to install Octave on CentOS.  On the bright 
side, Ubuntu can download Octave directly from the repository.  The downside is 
when I test my freesurfer install with tkmedit bert orig,mgz, I get the 
following error:

/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error.  Binary file not 
executable.

Is there is something additional I need to install because it is on Ubuntu?

Brian James
Technical Applications Analyst
North Bay Regional Health Centre
(705) 474-8600 x2611



The information contained in this electronic transmission is intended for the 
person(s) or entity to whom it is addressed. Delivery of this message to any 
person other than the intended recipient(s) is not intended in any way to waive 
confidentiality. This material may contain confidential or personal information 
which may be subject to the provisions of Ontario's Personal Health Information 
Protection Act. Any review, retransmission, dissemination or other use of this 
information by entities other than the intended recipient is prohibited. If you 
receive this in error, please contact the sender and delete the material 
immediately.

L'information contenue dans ce message électronique est destinée uniquement au 
destinataire ou aux destinataires visés. La transmission de ce message à une 
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Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

2011-12-30 Thread Ian Charest

Hi Brian

I had to change the terminal config for it to use tcsh.

I think Ubuntu now uses The Debian Almquist shell (dash) and I have had 
problems running freesurfer from it. 

install tcsh using aptitude and then in the preferences of your terminal (Edit 
> profile preferences) in the tab "title and command" click on "run custom 
command instead of my shell" and type /bin/tcsh as your custom command.

You can also set up some environment variables by editing the .tcshrc found in 
your home directory.

>gedit ~/.tcshrc

and add a modified version of this code according to where your freesurfer 
install is and where your subject directory lies...

alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv 
SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'

now if you close your terminal and open a new one, freesurfer should work.

Hope it helps

Ian


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of James, Brian 
[brian.ja...@nbrhc.on.ca]
Sent: 30 December 2011 20:40
To: martijnsteenw...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

That is what I did…my path is /usr/local/freesurfer

However, mine doesn’t seem to work.


Brian.


From: Martijn Steenwijk [mailto:martijnsteenw...@gmail.com]
Sent: December-30-11 2:37 PM
To: James, Brian
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10


Just untarring the .tar.gz in /usr/local like documented here 
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on 
Ubuntu 11.10.

Best,
Martijn


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens James, Brian
Verzonden: vrijdag 30 december 2011 21:13
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Everyone,
I thought I would try installing FreeSurfer on Ubuntu because I 
was having so many issues trying to install Octave on CentOS.  On the bright 
side, Ubuntu can download Octave directly from the repository.  The downside is 
when I test my freesurfer install with tkmedit bert orig,mgz, I get the 
following error:

/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error.  Binary file not 
executable.

Is there is something additional I need to install because it is on Ubuntu?

Brian James
Technical Applications Analyst
North Bay Regional Health Centre
(705) 474-8600 x2611



The information contained in this electronic transmission is intended for the 
person(s) or entity to whom it is addressed. Delivery of this message to any 
person other than the intended recipient(s) is not intended in any way to waive 
confidentiality. This material may contain confidential or personal information 
which may be subject to the provisions of Ontario's Personal Health Information 
Protection Act. Any review, retransmission, dissemination or other use of this 
information by entities other than the intended recipient is prohibited. If you 
receive this in error, please contact the sender and delete the material 
immediately.

L'information contenue dans ce message électronique est destinée uniquement au 
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The information contained in this electronic transmission is intended for the 
person(s) or entity to whom it is addressed. Delivery of this message to any 
person other than the intended recipient(s) is not intended in any way to waive 
confidentiality. This material may contain confidential or personal information 
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information by entities other than the intended recipient is prohibited. If you 
receive this in error, please contact the sender and delete the material 
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L'information contenue dans ce message électronique est destinée uniquement au 
destinataire ou aux destinataires visés. La transmission de ce message à une 
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d

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

2011-12-30 Thread James, Brian

That is what I did...my path is /usr/local/freesurfer

However, mine doesn't seem to work.


Brian.


From: Martijn Steenwijk [mailto:martijnsteenw...@gmail.com]
Sent: December-30-11 2:37 PM
To: James, Brian
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10


Just untarring the .tar.gz in /usr/local like documented here 
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on 
Ubuntu 11.10.

Best,
Martijn


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens James, Brian
Verzonden: vrijdag 30 december 2011 21:13
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Everyone,
I thought I would try installing FreeSurfer on Ubuntu because I 
was having so many issues trying to install Octave on CentOS.  On the bright 
side, Ubuntu can download Octave directly from the repository.  The downside is 
when I test my freesurfer install with tkmedit bert orig,mgz, I get the 
following error:

/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error.  Binary file not 
executable.

Is there is something additional I need to install because it is on Ubuntu?

Brian James
Technical Applications Analyst
North Bay Regional Health Centre
(705) 474-8600 x2611



The information contained in this electronic transmission is intended for the 
person(s) or entity to whom it is addressed. Delivery of this message to any 
person other than the intended recipient(s) is not intended in any way to waive 
confidentiality. This material may contain confidential or personal information 
which may be subject to the provisions of Ontario's Personal Health Information 
Protection Act. Any review, retransmission, dissemination or other use of this 
information by entities other than the intended recipient is prohibited. If you 
receive this in error, please contact the sender and delete the material 
immediately.

L'information contenue dans ce message électronique est destinée uniquement au 
destinataire ou aux destinataires visés. La transmission de ce message à une 
personne autre que son destinataire ou ses destinataires visés ne supprime en 
rien l'obligation d'en respecter la confidentialité. Ce message peut contenir 
des renseignements de nature confidentielle ou personnelle qui pourraient être 
soumis aux dispositions de la Loi de 2004 sur la protection des renseignements 
personnels sur la santé. L'examen, la retransmission, la diffusion et toute 
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autres que le destinataire ou les destinataires visés sont interdits. Si vous 
recevez ce message par erreur, veuillez le supprimer immédiatement et en 
avertir l'expéditeur.


The information contained in this electronic transmission is intended for the 
person(s) or entity to whom it is addressed. Delivery of this message to any 
person other than the intended recipient(s) is not intended in any way to waive 
confidentiality. This material may contain confidential or personal information 
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Protection Act. Any review, retransmission, dissemination or other use of this 
information by entities other than the intended recipient is prohibited. If you 
receive this in error, please contact the sender and delete the material 
immediately.

L'information contenue dans ce message électronique est destinée uniquement au 
destinataire ou aux destinataires visés. La transmission de ce message à une 
personne autre que son destinataire ou ses destinataires visés ne supprime en 
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soumis aux dispositions de la Loi de 2004 sur la protection des renseignements 
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Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

2011-12-30 Thread Martijn Steenwijk

 

Just untarring the .tar.gz in /usr/local like documented here
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm
on Ubuntu 11.10.

 

Best,

Martijn

 

 

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens James, Brian
Verzonden: vrijdag 30 december 2011 21:13
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10

 

Hi Everyone,

I thought I would try installing FreeSurfer on Ubuntu
because I was having so many issues trying to install Octave on CentOS.  On
the bright side, Ubuntu can download Octave directly from the repository.
The downside is when I test my freesurfer install with tkmedit bert
orig,mgz, I get the following error:

 

/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error.  Binary file
not executable.

 

Is there is something additional I need to install because it is on Ubuntu?

 

Brian James

Technical Applications Analyst

North Bay Regional Health Centre  

(705) 474-8600 x2611

 



The information contained in this electronic transmission is intended for
the person(s) or entity to whom it is addressed. Delivery of this message to
any person other than the intended recipient(s) is not intended in any way
to waive confidentiality. This material may contain confidential or personal
information which may be subject to the provisions of Ontario's Personal
Health Information Protection Act. Any review, retransmission, dissemination
or other use of this information by entities other than the intended
recipient is prohibited. If you receive this in error, please contact the
sender and delete the material immediately. 

L'information contenue dans ce message électronique est destinée uniquement
au destinataire ou aux destinataires visés. La transmission de ce message à
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supprimer immédiatement et en avertir l'expéditeur. 

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[Freesurfer] FreeSurfer & Ubuntu 11.10

2011-12-30 Thread James, Brian

Hi Everyone,
I thought I would try installing FreeSurfer on Ubuntu because I 
was having so many issues trying to install Octave on CentOS.  On the bright 
side, Ubuntu can download Octave directly from the repository.  The downside is 
when I test my freesurfer install with tkmedit bert orig,mgz, I get the 
following error:

/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error.  Binary file not 
executable.

Is there is something additional I need to install because it is on Ubuntu?

Brian James
Technical Applications Analyst
North Bay Regional Health Centre
(705) 474-8600 x2611



The information contained in this electronic transmission is intended for the 
person(s) or entity to whom it is addressed. Delivery of this message to any 
person other than the intended recipient(s) is not intended in any way to waive 
confidentiality. This material may contain confidential or personal information 
which may be subject to the provisions of Ontario's Personal Health Information 
Protection Act. Any review, retransmission, dissemination or other use of this 
information by entities other than the intended recipient is prohibited. If you 
receive this in error, please contact the sender and delete the material 
immediately.

L'information contenue dans ce message ?lectronique est destin?e uniquement au 
destinataire ou aux destinataires vis?s. La transmission de ce message ? une 
personne autre que son destinataire ou ses destinataires vis?s ne supprime en 
rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir 
des renseignements de nature confidentielle ou personnelle qui pourraient ?tre 
soumis aux dispositions de la Loi de 2004 sur la protection des renseignements 
personnels sur la sant?. L'examen, la retransmission, la diffusion et toute 
autre utilisation de l'information contenue dans ce message par des personnes 
autres que le destinataire ou les destinataires vis?s sont interdits. Si vous 
recevez ce message par erreur, veuillez le supprimer imm?diatement et en 
avertir l'exp?diteur.
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Re: [Freesurfer] Registration Error

2011-12-30 Thread Lilla Zollei


Hi Antonella,

> I have a problem with mri_cvs_register. I am getthing the following error and 
> I will be very grateful if you can help me to fix it (I am don't understand 
> what means this errors).

I suspect that you are running out of memory on your computer. Can you 
tell me the parameters of the machinethat you are using? Also, please, 
include the complete log file in your message as that will give us more 
details about the problem.

> Also, after running a group analysis with mri_glmfit-sim and using the option 
> --grf (so I have the survining clusters after multiple comparison) what is 
> the best way to do a comparison between two groups for my
> DTI data (more exactly I am interested in comparing the FA values)?

Have you looked at the significance maps that are resulting from such an 
analysis on your FA maps?

Lilla

> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Out of memory. This could be due to allocating
> [0]PETSC ERROR: too large an object or bleeding by not properly
> [0]PETSC ERROR: destroying unneeded objects.
> [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> [0]PETSC ERROR: Memory requested 779465992!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: surf2vol on a linux-gnu named EW-LNX2 by root Thu Dec 29 
> 14:34:49 2011
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
> [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in 
> src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>  ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to 
> find memory corruption
> errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: surf2vol on a linux-gnu named EW-LNX2 by root Thu Dec 29 
> 14:34:49 2011
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> 
> 
>
___
Freesurfer m

[Freesurfer] recon all problem

2011-12-30 Thread LAOUCHEDI MAKHLOUF

i looked in the .bashrc file and it is written : 
FREESURFER_HOME=/home/amesse/software/freesurfer5.1 ; 
      but  freesurfer is installed in another account to which  i have no 
access for the moment. i'll see it on monday 

thank you michael
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Re: [Freesurfer] aparc.a2009s+aseg problem

2011-12-30 Thread Michael Harms


You said initially that you were using FS v5.1, but that recon-
all.local-copy is not consistent with FS v5.1.

Are you processing subjects from scratch?  If so, then you need to check
your path/environment and figure out why an older version of recon-all
is being called when you think that you're using v5.1.

Please cc the list on communication so that the thread is captured in
the FS archives for others benefit.

cheers,
-MH

On Fri, 2011-12-30 at 16:52 +, LAOUCHEDI MAKHLOUF wrote:
> hi michael 
> in fact i gedited the recon-all.local-copy in
> /scripts and i noticed that the section "Cortical
> Parcellation 2 " contains references to a2005s and not to a2009s. is
> it a good idea to replace a2005s by a2009s in the text, then make a
> copy of the file and put it somewhere (my current directory for
> example) and then use it instead of the one given in
> /bin ?. then should i do the same modifications in
> the other parts of the text (for example the section "AParc2ASeg " and
> "Surface Anatomical Stats 2" ...) ?. 
>   i attached the recon-all.local-copy
> file.
> 
> thanks for all
> 
> --- En date de : Ven 30.12.11, Michael Harms 
> a écrit :
> 
> De: Michael Harms 
> Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
> À: "LAOUCHEDI MAKHLOUF" 
> Cc: freesurfer@nmr.mgh.harvard.edu
> Date: Vendredi 30 décembre 2011, 16h57
> 
> 
> For some reason the beginning section of the recon-all.log
> that you sent
> is missing (i.e,. the part containing the actual command that
> you ran).
> What was the exact recon-all command that you used?  From the
> log file,
> only the very first mri_convert was performed.  Was your
> command perhaps
> recon-all -i  -s 
> 
> If so, you need to include the -all flag to actually run all
> the rest of
> the recon-all stream.
> 
> cheers,
> -MH
> 
> 
> On Fri, 2011-12-30 at 13:55 +, LAOUCHEDI MAKHLOUF wrote:
> > Hi Michael
> > i looked in and the file doesn't contain a
> section
> > called "Cortical Parc 2" . what do you think is the
> problem ? i
> > attached the log
> > 
> > thanks
> > 
> > 
> > 
> > --- En date de : Jeu 29.12.11, Michael Harms
> 
> > a écrit :
> > 
> > De: Michael Harms 
> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
> > À: "LAOUCHEDI MAKHLOUF" 
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > Date: Jeudi 29 décembre 2011, 18h17
> > 
> > 
> > That is a job log from your cluster, which isn't
> helpful to
> > the issue at
> > hand.
> > 
> > You need to look in /scripts/recon-all.log,
> which
> > contains a
> > complete log of the entire recon-all processing
> stream.
> > 
> > cheers,
> > -MH
> > 
> > On Thu, 2011-12-29 at 17:10 +, LAOUCHEDI
> MAKHLOUF wrote:
> > > Hi Michael 
> > > i looked in the job.log file (i am
> using a
> > condor
> > > cluster) that i attached, and there is no such
> section!
> > > 
> > > thanks
> > > 
> > > --- En date de : Jeu 29.12.11, Michael Harms
> > 
> > > a écrit :
> > > 
> > > De: Michael Harms 
> > > Objet: Re: [Freesurfer] aparc.a2009s+aseg
> problem
> > > À: "LAOUCHEDI MAKHLOUF"
> 
> > > Cc: freesurfer@nmr.mgh.harvard.edu
> > > Date: Jeudi 29 décembre 2011, 18h01
> > > 
> > > 
> > > The problem is apparently that the
> > Xh.aparc.a2009s.annot
> > > wasn't created.
> > > 
> > > Look in scripts/recon-all.log and make
> sure that the
> > section
> > > "Cortical
> > > Parc 2" is present, and if it is, look for
> clues as
> > to why
> > > the .annot
> > > wasn't created.
> > > 
> > > cheers,
> > > -MH
> > > 
> > > On Thu, 2011-12-2

Re: [Freesurfer] fixing hemisphere leakage

2011-12-30 Thread Louis Nicholas Vinke

You could also look at the filled.mgz to see if the hemis are separated 
and potentially make some edits.  Then you would run:


recon-all -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2
-inflate2 -autorecon3 -s 

Lastly, you could set seed points for the corpus callosum using the 
-cc-crs flag.


https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits
-See the "seed points, fill and cut" section

-Louis

On Wed, 28 Dec 2011, David Groppe wrote:


Thanks for the speedy response Bruce.
I'm running:
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $

-David

On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl
 wrote:

Hi David

what version are you running?

Bruce

On Wed, 28 Dec 2011, David Groppe wrote:


Hi FreeSurfers,
 I'm trying to fix FreeSurfer's pial and white matter surface
boundary estimates on a brain missing a large part of the right
hemisphere.  I've manually filled in the greatly expanded ventricles
in the damaged hemisphere as white matter (see attached) and tried
rerunning recon-all with -autorecon2-wm and -autorecon3 flags.  This
fails to help.  Is there sometime else I can do?
    thanks in advance,
      -David





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[Freesurfer] Registration Error

2011-12-30 Thread Antonella Kis

Hi,

I have a problem with mri_cvs_register. I am getthing the following error and I 
will be very grateful if you can help me to fix it (I am don't understand what 
means this errors). 


Also, after running a group analysis with mri_glmfit-sim and using the option 
--grf (so I have the survining clusters after multiple comparison) what is the 
best way to do a comparison between two groups for my DTI data (more exactly I 
am interested in comparing the FA values)?


Many thaks and Happy New Year!
Antonella

[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
[0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 779465992!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: surf2vol on a linux-gnu named EW-LNX2 by root Thu Dec 29 
14:34:49 2011
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
[0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in 
src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: surf2vol on a linux-gnu named EW-LNX2 by root Thu Dec 29 
14:34:49 2011
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0___
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Re: [Freesurfer] aparc.a2009s+aseg problem

2011-12-30 Thread Michael Harms


For some reason the beginning section of the recon-all.log that you sent
is missing (i.e,. the part containing the actual command that you ran).
What was the exact recon-all command that you used?  From the log file,
only the very first mri_convert was performed.  Was your command perhaps
recon-all -i  -s 

If so, you need to include the -all flag to actually run all the rest of
the recon-all stream.

cheers,
-MH


On Fri, 2011-12-30 at 13:55 +, LAOUCHEDI MAKHLOUF wrote:
> Hi Michael
> i looked in and the file doesn't contain a section
> called "Cortical Parc 2" . what do you think is the problem ? i
> attached the log
> 
> thanks
> 
> 
> 
> --- En date de : Jeu 29.12.11, Michael Harms 
> a écrit :
> 
> De: Michael Harms 
> Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
> À: "LAOUCHEDI MAKHLOUF" 
> Cc: freesurfer@nmr.mgh.harvard.edu
> Date: Jeudi 29 décembre 2011, 18h17
> 
> 
> That is a job log from your cluster, which isn't helpful to
> the issue at
> hand.
> 
> You need to look in /scripts/recon-all.log, which
> contains a
> complete log of the entire recon-all processing stream.
> 
> cheers,
> -MH
> 
> On Thu, 2011-12-29 at 17:10 +, LAOUCHEDI MAKHLOUF wrote:
> > Hi Michael 
> > i looked in the job.log file (i am using a
> condor
> > cluster) that i attached, and there is no such section!
> > 
> > thanks
> > 
> > --- En date de : Jeu 29.12.11, Michael Harms
> 
> > a écrit :
> > 
> > De: Michael Harms 
> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
> > À: "LAOUCHEDI MAKHLOUF" 
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > Date: Jeudi 29 décembre 2011, 18h01
> > 
> > 
> > The problem is apparently that the
> Xh.aparc.a2009s.annot
> > wasn't created.
> > 
> > Look in scripts/recon-all.log and make sure that the
> section
> > "Cortical
> > Parc 2" is present, and if it is, look for clues as
> to why
> > the .annot
> > wasn't created.
> > 
> > cheers,
> > -MH
> > 
> > On Thu, 2011-12-29 at 16:03 +, LAOUCHEDI
> MAKHLOUF wrote:
> > > hi everyone 
> > >i run recon-all on 27 subjects
> using the
> > 5.1
> > > version, and i don't find  aparc.a2009s+aseg.mgz
> neither
> > > lh.aparc.a2009s.annot so i can't use the command
> > mri_aparc2aseg
> > > ( mri_aparc2aseg --s subject --a2009s). what must
> i do to
> > have
> > > aparc.a2009s+aseg.mgz.
> > > 
> > > thanks
> > > 
> > > ___
> > > 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
> > 
> 
> ___
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Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

[Freesurfer] FreeSurfer & Ubuntu 11.10

Re: [Freesurfer] Registration Error

[Freesurfer] recon all problem

Re: [Freesurfer] aparc.a2009s+aseg problem

Re: [Freesurfer] fixing hemisphere leakage

[Freesurfer] Registration Error

Re: [Freesurfer] aparc.a2009s+aseg problem

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