Freesurfer

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30084 discussions

Re: [Freesurfer] Exited with errors, segmentation fault
by Hoopes, Andrew 27 Oct '20

27 Oct '20

Hi Julia, This is a small bug that's been fixed in the 7.1.1 patch release. I would recommend updating freesurfer versions (there will be no differences in recon-all results). Best, Andrew On 10/13/20, 8:44 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Julia Lam" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of julia.lam(a)mau.se> wrote: External Email - Use Caution Hi, In one of 56 volumes, recon-all exited with errors (segmentation fault). I tried to rerun but received the same result. How can this be solved? I’ve attached the recon-all.log and recon-all.error. I am looking forward to your reply. Kind regards, Julia Lam

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Postdoctoral Fellowship
by Didenur Sahin 27 Oct '20

27 Oct '20

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800 -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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NIH funded postdoctoral position
by Ron Killiany 27 Oct '20

27 Oct '20

External Email - Use Caution Hi everyone, We have been fortunate to obtain funding for a postdoctoral position. A brief description is enclosed. Please feel free to pass this along to anyone who might be interested. --ron -- Ronald J. Killiany, Ph.D. Center for Biomedical Imaging Departments of Anatomy & Neurobiology, Neurology, Radiology and Environmental Health Boston University School of Medicine and Boston University School of Public Health 700 Albany Street, W701 Boston, Massachusetts 02118 *phone: 617-358-8276* fax: 617-638-4922

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Re: [Freesurfer] freeview Core Dumped Error after upgrade in ubuntu
by fsbuild 27 Oct '20

27 Oct '20

External Email - Use Caution Hello Antonin, I’ve found a few posts that seem to indicate you can upgrade as well as downgrade the kernel (and its dependent packages) by editing the /etc/apt/sources.list to point to the Ubuntu distribution you want (and then running update, upgrade, dist-upgrade commands)..   Not sure what the previous Ubuntu distribution name was for you, but this post, https://sypalo.com/how-to-upgrade-ubuntu, lists the distributions as, 18.04 - bionic 18.10 - cosmic 19.04 - disco 19.10 - eoan 20.04 - focal 20.10 - groovy While that post gives the example of *upgrading*, this post gives the example of *downgrading*, https://linuxconfig.org/how-to-downgrade-ubuntu-linux-system-to-its-previous-version, but I think they are essentially doing the same thing, i.e. it’s a function of the distribution name listed in /etc/apt/sources.list. Note that even if you are downgrading the kernel, as far as the apt package manager is concerned you still have to run the various “upgrade” commands to change the distribution to a different one even if it is older. - R. On Oct 26, 2020, at 11:00, Rovai Antonin <Antonin.Rovai(a)erasme.ulb.ac.be> wrote:       External Email - Use Caution        Dear experts,I use to have a perfectly working freesurfer installation on my Ubuntu18.04 LTS machine, until that doomsday where I installed updates asrecommended by ubuntu itself.Now, each time I run freeview, I get the following error:Aborted (core dumped)I reinstalled freesurfer from scratch, fixing nothing.I think Ubuntu did a kernel upgrade; now I have a uname -r output =5.4.0-52-genericI think it used to be 49 instead of 52 before the upgrade, but I am notsure.Do you know of any patch fixing this, by any chance?Thanks for your lightsAntonin RovaiHôpital Erasme - ULBCliniques universitaires de BruxellesRoute de Lennik 808 - B - 1070 BruxellesS www.erasme.ulb.ac.beDisclaimer : http://www.erasme.ulb.ac.be/email-disclaimer_______________________________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tracula error: run list is longer than subject list
by Shanika Jayakody 26 Oct '20

26 Oct '20

External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the error is about. I wonder if anyone can help me figure out a solution. Many thanks Oshadi

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segmentHA on Human Connectome Project
by AmirHussein Abdolalizadeh 26 Oct '20

26 Oct '20

External Email - Use Caution Hi, I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions: 1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline ( https://github.com/Washington-University/HCPpipelines) 2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject. 3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9). I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required. Bests, Amir

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Traculina availability
by Ngoh Zhen Ming 26 Oct '20

26 Oct '20

External Email - Use Caution Good Morning! I understand that the stable release of TRACULInA will be included in the next version of freesurfer. Is there an estimate of when that will be? Or if there are any versions that are currently openly available for trial? Thank you and look forward to hearing back! Zhen Ming, NGOH This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

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freeview Core Dumped Error after upgrade in ubuntu
by Rovai Antonin 26 Oct '20

26 Oct '20

External Email - Use Caution Dear experts, I use to have a perfectly working freesurfer installation on my Ubuntu 18.04 LTS machine, until that doomsday where I installed updates as recommended by ubuntu itself. Now, each time I run freeview, I get the following error: Aborted (core dumped) I reinstalled freesurfer from scratch, fixing nothing. I think Ubuntu did a kernel upgrade; now I have a uname -r output = 5.4.0-52-generic I think it used to be 49 instead of 52 before the upgrade, but I am not sure. Do you know of any patch fixing this, by any chance? Thanks for your lights Antonin Rovai Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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Re: [Freesurfer] Contents of Freesurfer digest Vol 200, Issue 28 error trac all prep (Yendiki, Anastasia)
by Camerino, I.L. (Ileana) 26 Oct '20

26 Oct '20

External Email - Use Caution Hi Anastasia, Thank you so much for your reply. I omitted a very important information. I am working with left hemisphere stroke data. On a visual check I see that recon all worked well on all the participants (big and small lesions). Although trac all worked for some participants with a smaller lesion, I suspect this failure may be due to the presence of a bigger lesion. In order to test if this is the case, I could perform trac all only on the right hemisphere. Can you tell me how to perform tracall only on the right hemisphere? I tried to edit the config file but it did not work. Please, let me know if you have other suggestions on what can go wrong as well. Thank you in advance Best regards Ileana Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618 On 14/10/2020, 18:01, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: error trac all prep (Yendiki, Anastasia) 2. Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed} (Jieyin Feng) 3. Help with creating contrast matrix - 6 classes and 3 variables (Paul Dhami) 4. Reliability and sensitivity of two whole-brain segmentation approaches ? ASEG and SAMSEG (Donatas Sederevicius) 5. tk applications failing to launch on VM (Windows) (Mcnorgan, Christopher) ---------------------------------------------------------------------- Message: 1 Date: Tue, 13 Oct 2020 20:20:03 +0000 From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] error trac all prep To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB57575E2B4044A5177DC947F08A040(a)MN2PR04MB5757.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Ileana - It looks like it fails on the left uncinate. Is there any artifact or missing part of the brain or brain mask, either in the diffusion scan or the T1 scan, in a location that would affect the uncinate? Anastasia. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Camerino, I.L. (Ileana) <i.camerino(a)psych.ru.nl> Sent: Tuesday, October 13, 2020 11:12 AM To: Freesurfer(a)nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] error trac all prep External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the tractography analyses as described on the Tracula tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula) I tried the all pipeline for one subject and it worked. I tried to run in parallel for the rest of the subjects and for three of them I get the following error when I run the trac all -prep command: #!/bin/bash export FREESURFER_HOME=/opt/freesurfer/6.0; source $FREESURFER_HOME/SetUpFreeSurfer.sh; export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer for i in `cat /project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do trac-all -prep -c /project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt; done here below the content of trac-all.eror ------------------------------ SUBJECT sub-056 DATE Fri Oct 9 16:18:01 CEST 2020 USER ilecam HOST dccn-c029.dccn.nl PROCESSOR x86_64 OS Linux Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $ /opt/freesurfer/6.0/bin/trac-preproc PWD /project/3015068.01/ilecam/Reolang/scripts CMD /opt/freesurfer/6.0/bin/dmri_train --outdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-056.18934.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.b! br.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dl! abel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.b! br.nii.g z dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni/aparc+aseg_mask.nii.gz --fa /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/dtifit_FA.nii.gz --cptdir /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/diff --reg /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dmri/xfms/mni2diff.bbr.mat --ncp! ts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc I've searched the list and no similar errors have been reported. Please can anyone share their thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer/6.0 build-stamp.txt: Platform: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2) 3) uname -a: Linux dccn-c046.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux) recon-all.log: see attached thank you in advance Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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Subject cluster mean values from ocn.dat do not show the expected group difference
by Julian Macoveanu 26 Oct '20

26 Oct '20

External Email - Use Caution Hi, I am using FS 7.1.0. After running the surface thickness GLM analysis I get one cluster after correction for multiple comparison showing a significant group difference. I want to make a plot illustrating this group difference. However, when using the mean values from: cache.th30.abs.y.ocn.dat, I don’t see the expected group difference in these values. Question 1) Are the subjects cluster mean values in y.ocn.dat adjusted for the covariates I used in the fsgd file? E.g. age, sex and TIV? Question 2) I inserted these mean cluster values from y.ocn.dat in SPSS and tried verify the statistics both with and without adjustment for covariates and did not get the expected significant group region which I expected in either case. Why is this? Question 3) I moved on to extract the thickness values from peak vertex in my significant cluster. For this I used mris_convert which I just wanted to be confirmed that is correct: mris_convert -c lh.thickness.fwhm15.fsaverage.mgh $freesurferdir/fsaverage/surf/lh.orig output.asc After extracting the thickness value for all subjects from the peak vertex as reported by the sig.cluster.summary, I still have the same issue as before, I find no expected group difference. Interestingly, the significant cluster I found is part of the superior_frontal region in aparc2009. When I extract these values it almost shows significant group differences in the entire region, in line with the surface GLM findings. Thanks, Julian

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