Dear Bruce and Jürgen,
Now I see something important which may help solving the problem.
I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04. 30
PCs were able to process all 47 subjects successfully. But failed to process
the remaining 8 subjects. Fortunately, one PC is installed with UBUNTU
13.01. I managed to installed the tcsh and csh after update and then run two
of the failed subjects so far successfully. I concluded it is the
installation version of UBUNTU. So 13.01 works fine but not 14.04.
I tried to re-install 13.01 on another PC, and I did that successfully.
However, but when I come to install the tcsh, after update it fails and it
says it is unable to locate the package tcsh (the reason is that 13.01 has
not longer packages to download.
As a summary,
one PC with 13.01 UBUNTU is running OK (but with the tcsh installed)
another OC with 13.01 is not running because I was not able to install tcsh
after update
I am now think of copying the tcsh from one pc to the 13.01 PC to make it
running but still trying.
I think as Bruce said, it is something wrong with the installation as the
quality is fine.
I hope I was able to clarify the problem and hope to receive any helpful
answer.
Many thanks in advance
Ali
On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi
Jürgen and Ali
I don't think it has anything to do with the quality of the data, but
we are also happy to take a look if you upload one subject. This seems
more like an installation issue, and I would think it would happen on
every subject. Did someone upgrade perl at somepoint? Or just some
paths?
cheers
Bruce
On Sun, 30 Aug 2015, Jürgen Hänggi wrote:
Dear Ali
instead of downgrading perl you can use the perlbrew tool
that allow to
install several perls in parallel and switch between perl
versions.
if you are able to install perl 5.12 (perlbrew install
5.12, you can see the
available perl versions with perlbrew available) and then
use
perlbrew use 5.12 before running recon-all in the
terminal.
Does it work?
Cheers
Jürgen
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Division Neuropsychology
Institute of Psychology
University of Zurich
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Von: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Ali Radaideh
<ali.radai...@hu.edu.jo>
Antworten an: Freesurfer Mailinglist
<freesurfer@nmr.mgh.harvard.edu>
Datum: Samstag, 29. August 2015 15:56
An: Freesurfer Mailinglist
<freesurfer@nmr.mgh.harvard.edu>
Betreff: Re: [Freesurfer] MRITOTAL
Dear Jürgen,
Thanks for your reply. Could you please guide me on how to
downgrade
it? I need to try everything with these 8 subjects to
finish the whole
cohort of subjects.
Your help is so appreciated.
Thanks,
Ali
On Sat, Aug 29, 2015 at 4:16 PM, Jürgen Hänggi
<j.haen...@psychologie.uzh.ch> wrote:
Dear Ali
if Talairach alignment is not of good quality, then
mritotal is
used and the shellwords.pl problem is related to the fact
that
you have a newer version of perl that no longer contain
shellwords.pl.
you can downgrade perl to 5.12 or so, which however, is
not a
good idea.
I have no other solution
Cheers
Jürgen
Von: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Ali
Radaideh <ali.radai...@hu.edu.jo>
Antworten an: Freesurfer Mailinglist
<freesurfer@nmr.mgh.harvard.edu>
Datum: Samstag, 29. August 2015 13:41
An: Freesurfer Mailinglist
<freesurfer@nmr.mgh.harvard.edu>
Betreff: [Freesurfer] MRITOTAL
Dear FreeSurfer experts,
I have sent email 10 days ago asking for a help with
processing 8 out of 55 subjects who failed to pass the
Talairach phase and gave me the following error:
tmpdir is transforms/tmp.talairach.5272
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/
MS_patients/freesurfer_test/Images_test/Samer/mri
mri_convert orig_nu.mgz
transforms/tmp.talairach.5272/src.mnc
mri_convert orig_nu.mgz
transforms/tmp.talairach.5272/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp $
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.5272/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg
-protocol icbm transforms/tmp.talairach.5272/src.mnc
transforms/talairach.auto.xfm
Can't locate shellwords.pl in @INC (@INC contains:
/usr/local/freesurfer/mni/bin/../lib/mni_autoreg
/usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2
/usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18
/usr/share/perl/5.18 /usr/local/lib/site_perl .) at
/usr/local/freesurfer/mni/bin/mritotal line 460.
ERROR: mritotal failed, see transforms/talairach.log
Linux ali-XPS-L501X 3.19.0-27-generic #29~14.04.1-Ubuntu
SMP Sun Aug 16 01:51:13 UTC 2015 x86_64 x86_64 x86_64
GNU/Linux
recon-all -s Samer exited with ERRORS at Sat Aug 29
07:27:06 EDT 2015
For more details, see the
logfile/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FI
LES/
MS_patients/freesurfer_test/Images_test/Samer/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Please, is there any way I can force this phase to run? I
have checked the images and they look fine but I dont know
why they failed.
Please your response is so important to my project as
everything is pending.
Many thanks in advance
Ali
--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
_______________________________________________ Freesurfer
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--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
_______________________________________________ Freesurfer
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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.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
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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.
--
Ali M. Al-Radaideh. PhD
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
