Dear hcp-users, I have aproblem using the freesurfer pipeline: It seems that the pipeline requires an old version of perl. Is there already a new script that contains the steps including the latest version of perl? The command "defined @array" produces this error. We found that this command is deprecated. Please see the output:
/Test/VP_101/101/T1w/101/mri /documents/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux pc1011 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 ( tel:491302) (2018-10-27) x86 ( tel:2018102786) _64 GNU/Linux Wed Jan 23 11:16:24 CET 2019 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 ( tel:20100220) at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.13847 /Test/VP_101/101/T1w/101/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13847/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13847/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2400.00 ( tel:240000) , 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.13847/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jan 23 11:16:26 CET 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.13847/nu0.mnc ./tmp.mri_nu_correct.mni.13847/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13847/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /documents/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct If we delete the command "defined @array" we get this error report: /Test/VP_101/101/T1w/101/mri /documents/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux pc10116 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 ( tel:491302) (2018-10-27) x86 ( tel:2018102786) _64 GNU/Linux Wed Jan 23 11:37:57 CET 2019 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 ( tel:20100220) at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.17117 /media/heg01017/schwarz/Test/VP_101/101/T1w/101/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17117/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17117/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2400.00 ( tel:240000) , 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) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17117/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jan 23 11:37:59 CET 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.17117/nu0.mnc ./tmp.mri_nu_correct.mni.17117/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17117/0/ -iterations 1000 -distance 50 [/Test/VP_101/101/T1w/101/mri/] [2019-01-23 11:37:59] running: /documents/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17117/0/ ./tmp.mri_nu_correct.mni.17117/nu0.mnc ./tmp.mri_nu_correct.mni.17117/nu1.imp Unquoted string "mnc" may clash with future reserved word at /documents/freesurfer/mni/bin/sharpen_volume line 153. syntax error at /documents/freesurfer/mni/bin/sharpen_volume line 153, near "=~ ?" Execution of /documents/freesurfer/mni/bin/sharpen_volume aborted due to compilation errors. nu_estimate_np_and_em: crashed while running sharpen_volume (termination status=65280) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Thank you so much for any kind of help - in advance! All the best from Germany, Gina M.Sc. Gina-Isabelle Henze Institut für Psychologie Lehrstuhl für Medizinische Psychologie, Psychologische Diagnostik und Methodenlehre Universitätsstrasse 31 Universität Regensburg 93053 Regensburg Tel.: +49-941-943-5645 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
