Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Research Opportunity
by Nillo, Ryan Michael R 29 Oct '18

29 Oct '18

External Email - Use Caution UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a multi-disciplinary approach to pursue neurodegenerative and neurodevelopment research. The candidate should have a strong statistical/computational background with experience with data analytic tools such as Matlab, R, and PLINK and potentially, MRI image analysis tools such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting immediately. Salary is commensurate with qualifications and experience. Job Requirements: 1.CV/NIH biosketch (must contain previous research experience) 2.Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3.Three references If interested please contact Dr. Leo Sugrue at leo.sugrue(a)ucsf.edu<mailto:leo.sugrue@ucsf.edu> Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] cluster failing on HCP freesurfer script
by Glasser, Matthew 29 Oct '18

29 Oct '18

External Email - Use Caution What version of FreeSurfer are you using? Is the FreeSurfer environment set up correctly? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Sanchez, Juan (NYSPI)" <Juan.Sanchez(a)nyspi.columbia.edu<mailto:Juan.Sanchez@nyspi.columbia.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, October 26, 2018 at 3:12 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] cluster failing on HCP freesurfer script External Email - Use Caution Dear community, My group is using the latest version of condor clustering to process our data on OS X. We have a bash script that calls freesurfer to run our HCP pipelines. I can run the script to completion when running it locally on each of the clustered machines, however when submitting the job I get the following error Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. (standard_in) 2: comparison in expression Can anyone suggest a solution? Thanks J ________________________________ 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.

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subfield normalization vs. covarying for whole hippocampal volume
by Lauren Salminen 29 Oct '18

29 Oct '18

External Email - Use Caution Hello, I’m working on a multi-site hippocampal subfields project (FSv. 6) and am wondering if it is “better” to normalize subfield volumes by dividing each subfield by whole hippocampal volume, or covary for hippocampal volume as an independent predictor variable in the regression models. Ultimately the goal is to determine the degree that each subfield may be uniquely associated with my target predictor variable, and we would like to know if this effect can be observed independent of potential differences in the whole hippocampus. Traditionally we have covaried for whole hippocampal volume, but I’ve found more interesting effects by normalizing each subfield to their hippocampal volume. Any guidance is appreciated. Thank you! ____________________ Lauren E. Salminen, Ph.D. Imaging Genetics Center Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California http://igc.ini.usc.edu/ <http://igc.ini.usc.edu/>

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Re: [Freesurfer] cluster failing on HCP freesurfer script
by fsbuild 29 Oct '18

29 Oct '18

External Email - Use Caution Mac OS comes with perl 5.18.  The module MNI/Startup.pm is not part of standard perl, and so it is provided in the freesurfer distribution.  When you source either the FreeSurferEnv.csh or FreeSurferEnv.sh script the environment variable MNI_PERL5LIB should get set to $FREESURFER_HOME/mni/lib/../Library/Perl/Updates/5.12.3   You should be able to ls that path and see an MNI Perl module there, i.e., the file MNI.pm. Subsrquently, the FreeSruferEnv scripts add MNI_PERL5LIB into the environment variable PERL5LIB.   But if something in the cluster environment is unsetting/setting PERL5LIB after FreeSurferEnv runs, then freesurfer will not be able to find the module.  You need to check the (final) values of MNI_PERL5LIB  and  PERL5LIB in the cluster environment.

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FreeSurfer error at selxavg3-sess
by elahe' yargholi 27 Oct '18

27 Oct '18

External Email - Use Caution Dear FreeSurfer developers, I have an fMRI data and using the command “selxavg3-sess -s ./SM/Analysis_3_12 -analysis BioMot_Block_RL_self0m.rh -run-wise -no-con-ok”, analysis of right hemisphere is finished correctly. While for the analysis of left hemisphere as I run “selxavg3-sess -s ./SM/Analysis_3_12 -analysis BioMot_Block_RL_self0m.lh -run-wise -no-con-ok”, I receive the following error: … $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /Users/elaheyargholi/Documents/Action_Project/July_2018/SM Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 12, skipping 1 Colors_RGB.mat Reference to non-existent field 'RmPreStim'. Error in fast_ldanaflac (line 518) flac.con(nthcon).rmprestim = cspec.RmPreStim; % 4/8/09 Error in fast_selxavg3b (line 107) flac0 = fast_ldanaflac(analysis); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n It should be mentioned that flags of mkanalysis-sess have the same values for both hemispheres. I do appreciate your attention. Best Regards, Elahe'

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Cerebellum Segmentation
by Min Zhang 26 Oct '18

26 Oct '18

External Email - Use Caution HI， Freesufer Team I want to try to segment the Cerebellum from the Brain MRI, does the freesurfer support the cerebellum segmentation? and how to process it? Many Thanks! Best Min

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cluster failing on HCP freesurfer script
by Sanchez, Juan (NYSPI) 26 Oct '18

26 Oct '18

External Email - Use Caution Dear community, My group is using the latest version of condor clustering to process our data on OS X. We have a bash script that calls freesurfer to run our HCP pipelines. I can run the script to completion when running it locally on each of the clustered machines, however when submitting the job I get the following error Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. (standard_in) 2: comparison in expression Can anyone suggest a solution? Thanks J

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Re: [Freesurfer] Error in segmentHA_T1.sh
by Scheffler, F, Mev [fredas＠sun.ac.za] 26 Oct '18

26 Oct '18

External Email - Use Caution Sorry, scratch that. Apparently it just didn’t realise that my subjects were in a subdirectory in the subjects directory. Running now. Note to self: “Think before you click send” Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Scheffler, F, Mev [fredas(a)sun.ac.za]" <fredas(a)sun.ac.za> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 26 October 2018 at 18:24 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in segmentHA_T1.sh External Email - Use Caution Dear Freesurfer Developers I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well. It sets up the environment and then complains about myMRIread and Error in segmentSubjectT1_autoEstimateAlveusML (line 157) Here is the command line output: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is <redacted, because I’m paranoid> Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 157) @#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 33416 O 0 L 0.02 5.50 14.86 @#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.78 4.16 13.38 Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018 What am I doing wrong here? Thanks very much. Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer%20> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer%20>

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Segmentation fault
by Whitney, Jon 26 Oct '18

26 Oct '18

External Email - Use Caution Hey Freesurfer team, I'm working on running Tracula, and have been running into segmentation fault issues. We have consistently been running into segmentation fault issues. * The data we are working with comes from children*, and I'm concerned that differences in MRI image brightness and mapping between adult and children's brains may be throwing Tracula off. In many cases the typical pathlist of files ( lh.cst_AS, rh.cst_AS, etc) are not fully populated in the bedp step. We have therefore started submitting the job with the set pathlist and set ncpts to only point to files which are generated during the bedp step. Nonetheless, we are still getting segmentation fault errors during the final path step. I'm using freesurfer version 6.0.0-2beb96c, but I'm not sure what version of Tracula I'm using. This is a log of the error: Initial proposal SD file: /data/Abeona/W4WUM/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/Abeona/W4WUM/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Loading DWIs from /data/Abeona/W4WUM/dmri/dwi.nii.gz Loading mask from /data/Abeona/W4WUM/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /data/Abeona/W4WUM/dmri.bedpostX Loading b-values from /data/Abeona/W4WUM/dmri/bvals Loading gradients from /data/Abeona/W4WUM/dmri/bvecs INFO: Found 1 baseline images (b = 0) out of a total of 31 frames Segmentation fault (core dumped) Linux ip-10-0-0-222 4.4.0-137-generic #163-Ubuntu SMP Mon Sep 24 13:14:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Wed Oct 24 01:22:16 UTC 2018 The Freesurfer help I've looked at previous suggested that it could be a memory error, but we're using a remote drive that has lots of disk space and 26 GB RAM, so I doubt that's it. Checked the LANG, we are using en_US.UTF-8. I've run this on at least 8 different patients so far, and only one of them has not had this kind of error. Some of the different patients have different numbers of the normal path files exported into /dlabel/diff/, so it seems like there is patient-to-patient variability in how well the bedp phase is able to map things out. Thanks for your help! -Jon -- Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.

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Error in segmentHA_T1.sh
by Scheffler, F, Mev [fredas＠sun.ac.za] 26 Oct '18

26 Oct '18

External Email - Use Caution Dear Freesurfer Developers I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well. It sets up the environment and then complains about myMRIread and Error in segmentSubjectT1_autoEstimateAlveusML (line 157) Here is the command line output: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is <redacted, because I’m paranoid> Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 157) @#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 33416 O 0 L 0.02 5.50 14.86 @#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.78 4.16 13.38 Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018 What am I doing wrong here? Thanks very much. Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

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