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) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. --------------------------------------------------------------------------- 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 <http://shellwords.pl> problem is related to the fact that you >> have a newer version of perl that no longer contain shellwords.pl >> <http://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/M >>> S_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 <http://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/M >>> S_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 mailing list >>> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi >>> nfo/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. >> > > > > -- > 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 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.
