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
>>
>>
>>
>> ---------------------------------------------------------------------------
>> Jürgen Hänggi, Ph.D.
>>
>> Division Neuropsychology
>>
>> Institute of Psychology
>>
>> University of Zurich
>>
>> Binzmuehlestrasse 14, PO Box 25
>>
>> 8050 Zurich, Switzerland
>>
>> 0041 44 635 73 97 (phone office)
>>
>> 0041 76 445 86 84 (phone mobile)
>>
>> 0041 44 635 74 09 (fax office)
>>
>> BIN 4.D.04 (office room number)
>>
>> j.haenggi[at]psychologie.uzh.ch (email)
>>
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
>> http://www.juergenhaenggi.ch (private website)
>>
>>
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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 log
>> file/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/
>> 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=
>>
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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 mailing
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>> information in this e-mail is intended only for the person to whom it
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>> Compliance HelpLine at http://www.partners.org/complianceline . If the
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-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo <ali.radai...@hu.edu.jo>*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
<http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*
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