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 <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/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 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.
