Can anyone comment on a timeline for these fixes? In the meantime, does anyone know the exact version of Perl that broke FS 5.3_HCP? I may try to build a singularity container with an old enough version to work. From looking online it seems like it's somewhere around 5.16, but can't pin it down exactly.
-Mike -----Original Message----- From: Glasser, Matthew <glass...@wustl.edu> Sent: Thursday, February 07, 2019 11:14 PM To: Angstadt, Mike <mangs...@med.umich.edu>; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Problem with the freesurfer pipeline External Email - Use Caution I¹ll let the folks who are working on FS 6.0 HCP Pipelines integration comment on this. I know there is some testing continuing. Matt. On 2/7/19, 10:12 PM, "Angstadt, Mike" <mangs...@med.umich.edu> wrote: >Do you have an idea what timeframe this fix will be available in? We >are trying to run the HCP pipeline 3.27 version on some data, but just >ran into this issue as we are running Perl 5.22 on Ubuntu 16.04. Sounds >like the issue is fixed already in newer Freesurfer versions, but not >the version currently supported in the HCP pipeline. > >-Mike > > >________________________________________ >From: hcp-users-boun...@humanconnectome.org ><hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew ><glass...@wustl.edu> >Sent: Wednesday, January 30, 2019 6:37:42 PM >To: Gina Henze; hcp-users@humanconnectome.org >Subject: Re: [HCP-Users] Problem with the freesurfer pipeline > >External Email - Use Caution >There is a fix for this very soon to be available. > >Matt. > >From: ><hcp-users-boun...@humanconnectome.org<mailto:hcp-users-bounces@humanco >nne >ctome.org>> on behalf of Gina Henze ><gina.he...@psychologie.uni-regensburg.de<mailto:Gina.Henze@psychologie >.un >i-regensburg.de>> >Date: Wednesday, January 30, 2019 at 8:21 AM >To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" ><hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> >Subject: [HCP-Users] Problem with the freesurfer pipeline > >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<mailto:HCP-Users@humanconnectome.org> >http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >________________________________ >The materials in this message are private and may contain Protected >Healthcare Information or other information of a sensitive nature. If >you are not the intended recipient, be advised that any unauthorized >use, disclosure, copying or the taking of any action in reliance on the >contents of this information is strictly prohibited. If you have >received this email in error, please immediately notify the sender via >telephone or return mail. > >_______________________________________________ >HCP-Users mailing list >HCP-Users@humanconnectome.org >http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should >not be used for urgent or sensitive issues > ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
