Hi Leighton - This sounds like the perl problem identified on the FreeSurfer mail list... https://www.mail-archive.com/[email protected]/msg47059.html
The problem is that 'defined(@array)' was depreciated in previous versions of perl (so gave warnings only), but now generates an error and aborts. I investigated the two suggestions, but downgrading perl runs the risk of breaking lots of other things, while running the development version of FreeSurfer introduced more problems than it solved. My solution was to modify the perl scripts themselves as below: In /usr/local/freesurfer/mni/bin In sharpen_volume Line 153 add 'm' as below < ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) || --- > ($output_volume =~ m?^([\S]+).mnc?) && ($base_name = $1) || sudo sed -i -- 's/defined//g' nu_estimate_np_and_em sudo sed -i -- 's/defined//g' imp2field sudo sed -i -- 's/defined//g' field2imp sudo sed -i -- 's/defined//g' nu_estimate sudo sed -i -- 's/defined//g' nu_evaluate sudo sed -i -- 's/defined//g' resample_labels sudo sed -i -- 's/defined//g' sharpen_volume sudo sed -i -- 's/defined//g' xfmtool sudo sed -i -- 's/defined//g' nu_correct sudo sed -i -- 's/defined//g' mritotal sudo sed -i -- 's/defined//g' autocrop sudo sed -i -- 's/defined//g' mritotal sudo sed -i -- 's/defined//g' mritoself sudo sed -i -- 's/defined//g' mincpik sudo sed -i -- 's/defined//g' make_template Don't forget to make a backup of everything before you modify these files. This worked for me at least. Please let me know if it does the trick. Thanks - Richard Richard Watts, D.Phil. UVM MRI Center for Biomedical Imaging, McClure 1279 Fletcher Allen Healthcare 111 Colchester Avenue Burlington VT 05401 Telephone +1 802 829-9123 ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Wednesday, July 20, 2016 1:00 PM To: [email protected] Subject: HCP-Users Digest, Vol 44, Issue 22 Send HCP-Users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://lists.humanconnectome.org/mailman/listinfo/hcp-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of HCP-Users digest..." Today's Topics: 1. (standard in) 2: Error: comparison in expression (Leighton Barnden) 2. Re: (standard in) 2: Error: comparison in expression (Glasser, Matthew) 3. Connectome Research Coordinator (Senior), University of Pennsylvania (Jeff Phillips) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Jul 2016 14:18:51 +1000 From: Leighton Barnden <[email protected]> Subject: [HCP-Users] (standard in) 2: Error: comparison in expression To: [email protected] Cc: Krusty - Paul Jardine <[email protected]>, Zack Shan <[email protected]> Message-ID: <CAHkbBp3EXYn9t=1dRbA=nyr96d0s4ox2j66p9pv1idpogxb...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi HCP experts, When I run FreeSurferPipeLine.sh, I get the previously-mentioned ?"(standard in) 2: Error: comparison in expression" In /usr/share/fsl/5.0/bin/fsl_sub, from list suggestions, I've tried? commenting out POSIXLY_CORRECT=1 or adding ?unset POSIXLY_CORRECT? The last few lines of recon-all.log are mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux pc053865 4.4.0-31-generic #50-Ubuntu SMP Wed Jul 13 00:07:12 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MR002 exited with ERRORS at Wed Jul 20 12:06:43 AEST 2016 ?I'm running Ubuntu 16.04 and the recommended versions of FSL(5.0.9) and FreeSurfer ( freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP.tar.gz) Any suggestions on a way forward would be greatly appreciated. Thanks Leighton -- Leighton Barnden PhD Imaging Consultant, National Centre for NeuroImmunology and Emerging Diseases, Room 9.19 G40, Griffith University, Parklands Drive, Southport, QLD 4222, Australia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160720/aad9a25a/attachment-0001.html ------------------------------ Message: 2 Date: Wed, 20 Jul 2016 10:14:06 +0000 From: "Glasser, Matthew" <[email protected]> Subject: Re: [HCP-Users] (standard in) 2: Error: comparison in expression To: Leighton Barnden <[email protected]>, "[email protected]" <[email protected]> Cc: Krusty - Paul Jardine <[email protected]>, Zack Shan <[email protected]> Message-ID: <d3b4b911.120369%[email protected]> Content-Type: text/plain; charset="utf-8" That usually isn?t a fatal error. Are there any other errors? Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Leighton Barnden <[email protected]<mailto:[email protected]>> Date: Tuesday, July 19, 2016 at 11:18 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Cc: Krusty - Paul Jardine <[email protected]<mailto:[email protected]>>, Zack Shan <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] (standard in) 2: Error: comparison in expression Hi HCP experts, When I run FreeSurferPipeLine.sh, I get the previously-mentioned ?"(standard in) 2: Error: comparison in expression" In /usr/share/fsl/5.0/bin/fsl_sub, from list suggestions, I've tried? commenting out POSIXLY_CORRECT=1 or adding ?unset POSIXLY_CORRECT? The last few lines of recon-all.log are mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux pc053865 4.4.0-31-generic #50-Ubuntu SMP Wed Jul 13 00:07:12 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MR002 exited with ERRORS at Wed Jul 20 12:06:43 AEST 2016 ?I'm running Ubuntu 16.04 and the recommended versions of FSL(5.0.9) and FreeSurfer (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP.tar.gz) Any suggestions on a way forward would be greatly appreciated. Thanks Leighton -- Leighton Barnden PhD Imaging Consultant, National Centre for NeuroImmunology and Emerging Diseases, Room 9.19 G40, Griffith University, Parklands Drive, Southport, QLD 4222, Australia _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160720/2aecf414/attachment-0001.html ------------------------------ Message: 3 Date: Wed, 20 Jul 2016 12:23:38 -0400 From: Jeff Phillips <[email protected]> Subject: [HCP-Users] Connectome Research Coordinator (Senior), University of Pennsylvania To: [email protected] Message-ID: <CAM-Vdqo3xUvaxKbzpLhiB_-h30Boj_mE5RTM8=0h+us0714...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear colleagues, The Penn Frontotemporal Degeneration Center at the University of Pennsylvania is seeking a research coordinator for the multi-site FTD Connectome study. Please see the details below; applications should be directed to http://jobs.hr.upenn.edu/postings/18756. Thanks, Jeff Phillips Postdoctoral Fellow Penn FTD Center University of Pennsylvania Duties: The primary responsibility of the successful candidate will be the coordination of a multi-site consortium using a novel approach to neuroimaging of neurodegenerative diseases. The lead site is Penn, and participating sites include Mayo Clinic, UCSF, MGH and Northwestern. All sites have specialized neuroimaging equipment, and we will be using advanced neuroimaging tools developed locally and in collaboration with the Human Connectome Project (HCP) to analyze the acquired data. The successful candidate also will be responsible for managing the Penn site. This project is coordinated with two other multi-site registries involving these same sites that are recruiting participants for this neuroimaging project (and other studies). Participants will include: 1. healthy control subjects; 2. individuals who have a frontotemporal degeneration (FTD) spectrum disorder such as primary progressive aphasia, progressive supranuclear palsy, or FTD with amyotrophic lateral sclerosis; and 3. individuals who are carrying a mutation that has resulted in an FTD spectrum disorder or are at risk for developing a FTD-spectrum disorder. Coordination will include weekly meetings with project coordinators at the other participating sites, developing reports for monthly meetings with NIH and principal investigators at other sites, monitoring imaging data flow to our coordinating site, monitoring the database that tracks participants, monitoring data flow from Penn to the HCP coordinating center, and managing requests for data from investigators. Other administrative responsibilities will include help managing the consortium budget. Local site responsibilities will include assistance with on-going recruitment processes, helping to collect imaging data, managing the local budget, supervising local technical and research staff, and participating in imaging analyses. Also included are implementation of Connectome imaging analysis and operation of the Prisma MRI scanner. Position is contingent on continued funding. Qualifications: A Bachelor?s degree and to 3 to 5 years of experience, or equivalent combination of education and experience, are required. Masters degree or PhD in neuroscience, psychology, linguistics, biology, biomedical engineering or related fields and 2 years to 3 years of experience strongly preferred. Past research and project coordination experience working in a similar lab setting is highly desirable. Experience with the following is preferred: Linux/Unix, brain imaging data analysis, MATLAB, computer programming, statistical analysis, research project management, or neuropsychological assessment. The candidate must be able to work independently and have strong organizational and interpersonal skills. Apply at http://jobs.hr.upenn.edu/postings/18756 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160720/520e617f/attachment-0001.html ------------------------------ _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users End of HCP-Users Digest, Vol 44, Issue 22 ***************************************** This message and any attachments may contain information that is confidential, privileged and/or protected from disclosure under state and federal laws. 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