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. 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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