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30131 discussions

Error/shifting in cortical parcellation
by Helena-Céline Stevelt 15 Jun '21

15 Jun '21

External Email - Use Caution Dear Freesurfer Community, I wish to manually reassign/edit cortical parcellation performed by FS. We use the cortical parcellation done by FS and it has worked very well for most of our subjects. However, we have two subjects where the parcellation has not been done correctly. It seems that the central sulcus has been mis-classified to be one sulcus too far posterior in the brain - this has resulted in incorrect labeling of surrounding gyri. Curiously, it is only one hemisphere for both subjects (rh for one and lh for the other), where the other hemisphere is correctly parcellated. In our two mis-parcellated subjects, how might we manually reassign or guide FS to correctly classify the central sulcus and thus correctly label the surrounding gyri? I have attached a picture of an erroneous parcellation. Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a Platform: Ubuntu 16.04 Best, Helena-Céline Stevelt Danish Research Centre for Magnetic Resonance

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HIRING: Postdoc and Research Tech
by Zollei, Lilla,Ph.D. 15 Jun '21

15 Jun '21

I am hiring at the Martinos Center, MGH. For details, see 1. Postdoc: https://scholar.harvard.edu/lillazollei/jobs 2. Research technician: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3156502 If you have any questions, let me know. Best, Lilla

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the white matter surface is from the individual sMRI?
by 1248742467 14 Jun '21

14 Jun '21

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri？

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can the white matter surface is from the individual sMRI?
by 1248742467 14 Jun '21

14 Jun '21

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri？

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FreeSurfer cortical thickness
by Rosalia Dacosta Aguayo 14 Jun '21

14 Jun '21

External Email - Use Caution Dear Freesurfer's experts, I run FreeSurfer and I got the following stats: rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ ls aseg.stats lh.BA_exvivo.thresh.stats rh.aparc.stats lh.aparc.a2009s.stats lh.curv.stats rh.BA_exvivo.stats lh.aparc.DKTatlas.stats lh.w-g.pct.stats rh.BA_exvivo.thresh.stats lh.aparc.pial.stats rh.aparc.a2009s.stats rh.curv.stats lh.aparc.stats rh.aparc.DKTatlas.stats rh.w-g.pct.stats lh.BA_exvivo.stats rh.aparc.pial.stats wmparc.stats rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ A part from the aseg.stats file, which one should I consider if I am interested in cortical thickness. Should I run any other step for this? Best, Rosie

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Samseg pallidum issue
by Russo, Andrew William 14 Jun '21

14 Jun '21

Hello FreeSurfer Developers, I ran longitudinal samseg on a group of subjects with MS (each with 5 MRI timepoints over 2 years) and found that the average volume of the pallidum increased over time, while other subcortical volumes (caudate, putamen, thalamus) decreased. I also tried longitudinal samseg using the --pallidum-separate flag and had similar results. As the putamen gets smaller it looks like the pallidum volume grows to fill in the space. Have you encountered this issue before? I am using enhanced T1 images (made from T1, FLAIR, and FA data) as the input for run_samseg_long (FreeSurfer v7). Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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TRACULA trac-all cores/threads
by Drucker, Daniel 13 Jun '21

13 Jun '21

trac-all (TRACULA) seems to use multiple threads/cores. Is there a way to either (a) limit the number, or (b) determine how many it will use, so it can behave appropriately in a cluster? -- Daniel M. Drucker, Ph.D. Director of IT McLean Hospital Imaging Center Harvard Medical School

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Inquiry about creating .label files from .nii file
by Evan Collins 13 Jun '21

13 Jun '21

External Email - Use Caution FreeSurfer, I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files? Thank you.

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Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"
by Chester Kang 12 Jun '21

12 Jun '21

External Email - Use Caution Hi Eugenio, Yes, Matlab runtime had already been installed. Copying initial description of checks/troubleshooting already done so far, "... > Things that have been checked/tried or troubleshooting attempted: > - SIP protection is disabled (csrutil status shows "disabled") > - Checked that there are files and correct permissions in the "lib/gcc/lib" > and the "MCRv84" folders > - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh) > - checked the DYLD_LIBRARY_PATH value and run a step directly (both with "" > empty value and the values below) ..." Hope to that helps! Regards, Chester ------------------------------ Message: 4 Date: Fri, 11 Jun 2021 11:43:21 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded" To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <E7200246-C4B9-4198-ADEE-0B5F4A8C8C13(a)mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Thanks, Chester, that looks good. Am I safely assuming that the Matlab runtime has been installed? Cheers, /Eugenio > On 10 Jun 2021, at 21:31, Chester Kang <ckkang(a)unimelb.edu.au> wrote: > > External Email - Use Caution > > Hi Eugenio, > > The command that was run is segmentHA_T1.sh. > > I've rerun and copy-n-pasted the entire session below. > > "... > > chesterk@selma:~$ source SetUpFreeSurfer_mac.sh > -------- freesurfer-darwin-macOS-7.1.0-20200511-813297b -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer_v7.1.0 > FSFAST_HOME /Applications/freesurfer_v7.1.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Users/chesterk/subjects > MNI_DIR /Applications/freesurfer_v7.1.0/mni > FSL_DIR /usr/local/fsl_v6.0.4 > chesterk@selma:~$ cd subjects > chesterk@selma:~/subjects$ segmentHA_T1.sh 1001126copy > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12 > AEST > ------------------------------------------ > Setting up environment variables > --- > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free > surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy > s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees > urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib > /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus > ML.sh: line 33: > /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a > pp/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or > directory > Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue > Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 > > > T1 hippocampal subfields exited with ERRORS at Fri 11 Jun 2021 11:25:12 > AEST > > > For more details, see the log file > /Users/chesterk/subjects/1001126copy/scripts/hippocampal-subfields-T1.log > > > chesterk@selma:~/subjects$ more > 1001126copy/scripts/hippocampal-subfields-T1.log > ------------------------------ > USER chesterk > HOST selma.nnf.unimelb.edu.au > PROCESSID 37954 > PROCESSOR x86_64 > OS Darwin > ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 > Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue > Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 > ------------------------------ > > freesurfer-darwin-macOS-7.1.0-20200511-813297b > > setenv SUBJECTS_DIR /Users/chesterk/subjects > cd /Users/chesterk/subjects > /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1001126copy > > > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12 > AEST > ------------------------------------------ > Setting up environment variables > --- > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free > surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy > s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees > urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib > /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus > ML.sh: line 33: > /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a > pp/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or > directory > Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue > Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 > > > T1 hippocampal subfields exited with ERRORS at Fri 11 Jun 2021 11:25:12 > AEST > > > ..." > > Please let me know if I can provide any other details. > Thanks! > > > Regards, > Chester > > > > > > On 10/6/21, 12:51 am, "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: > >> External email: Please exercise caution >> >> Send Freesurfer mailing list submissions to >> freesurfer(a)nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://secure-web.cisco.com/11QCqR7prxSgfCTvoUKKRK8tL2ls0hM_Sfukn_muBU55xc… >> .mgh.harvard.edu >> 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: Hippocampal Subfields error "no such file or >> directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.) >> 2. Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy) >> 3. LGI FS 7.1 (Del Re, Elisabetta) >> 4. mri_glmfit with pvr (stdp82(a)virgilio.it) >> 5. Re: FW: WM or Pial edits to correct surfaces (Fischl, Bruce) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 9 Jun 2021 12:24:19 +0000 >> From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> >> Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or >> directory"/"dyld library not loaded" >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Message-ID: <8419D11C-C916-4249-9983-557A252291EC(a)mgh.harvard.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> Dear Chester, >> What command did you exactly run? There seems to be a mix of T1 and >> T1+additionalMRI segmentation commands in there. >> Cheers, >> /Eugenio >> >> Juan Eugenio Iglesias >> Senior research fellow >> CMIC (UCL), MGH (HMS) and CSAIL (MIT) >> http://secure-web.cisco.com/1qi_706jGqyyM3M3yDYUokzl_m0IkJHWaqcVYgXiltKvmf2… >> s.com >> >>> On Jun 9, 2021, at 00:23, Chester Kang <ckkang(a)unimelb.edu.au> wrote: >>> >>> External Email - Use Caution >>> >>> Hello FreeSurfer Developers, >>> >>> I am trying to run subfield segmentation of the hippocampus using >>> Freesurfer v7.1.0. Recon-all has been previously run on all subjects, >>> however with a different version of Freesurfer (v5.3.0). >>> >>> Getting the error(s): "No such file or directory" and on further >>> investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib" >>> >>> I've searched the archive but could not find a solution. >>> >>> Could someone please help? >>> >>> Below are details of the system and unsuccessful troubleshooting >>> attempts. >>> >>> Regards, >>> Chester >>> >>> >>> FreeSurfer version: 7.1.0 >>> Platform: Mac OS 10.13.3 >>> hippocampal-subfields-T1.log is below: >>> >>> Things that have been checked/tried or troubleshooting attempted: >>> - SIP protection is disabled (csrutil status shows "disabled") >>> - Checked that there are files and correct permissions in the >>> "lib/gcc/lib" and the "MCRv84" folders >>> - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh) >>> - checked the DYLD_LIBRARY_PATH value and run a step directly (both >>> with "" empty value and the values below) >>> >>> $ echo $DYLD_LIBRARY_PATH >>> >>> >>> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr >>> eesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib >>> /gcc/lib >>> >>> $ >>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus >>> ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML >>> >>> >>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus >>> ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML >>> dyld: Library not loaded: @rpath/libmwlaunchermain.dylib >>> Referenced from: >>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus >>> ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML >>> Reason: image not found >>> Abort trap: 6 >>> >>> >>> >>> === hippocampal-subfields-T1.log === >>> >>> >>> "... >>> ------------------------------ >>> USER chester >>> HOST selma.nnf.unimelb.edu.au >>> PROCESSID 17656 >>> PROCESSOR x86_64 >>> OS Darwin >>> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 >>> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: >>> Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 >>> ------------------------------ >>> >>> freesurfer-darwin-macOS-7.1.0-20200511-813297b >>> >>> setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all >>> cd /data/netapp02/work/chester/global_pass_all >>> /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310 >>> >>> #-------------------------------------------- >>> #@# Hippocampal Subfields processing (T1) left Tue 8 Jun 2021 15:25:15 >>> AEST >>> ------------------------------------------ >>> Setting up environment variables >>> --- >>> DYLD_LIBRARY_PATH is >>> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr >>> eesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84 >>> //sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib >>> >>> /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlve >>> usML.sh: line 33: >>> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML >>> .app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file >>> or directory >>> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: >>> Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 >>> >>> T1 hippocampal subfields exited with ERRORS at Tue 8 Jun 2021 15:25:16 >>> AEST >>> >>> ..." >>> >>>

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Re: [Freesurfer] memory allocation error
by Bernardoni, Fabio 11 Jun '21

11 Jun '21

External Email - Use Caution Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached): https://secure-web.cisco.com/1Ip5HtCg9MqyghYHl20NFxCMImoJoShIH1y6ytQEK2tKtD… my FS version is: recon-all -version freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e and I did not perform any editing, so there is no control points to remove as suggested in the above post (which also refers to version 6). Therefore, if I understand correctly, my problem is a different one. Any clue what I might be doing wrong? Other possibly useful information: uname -a Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux Thanks for any hint/help Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/15HwLpU5VlSqNSJlIROcqXzy17m5cEVlxA22c1BhqN_Pd35…; http://secure-web.cisco.com/1jdKs38Kd-Oms54JIKsH7_jGGI6wne-La9XILjLrzWQA_Nw… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1MMyCALLCSmaFUzZQnggtv4g0CsExa-ayBmQqe80VwC13pQ… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1MMyCALLCSmaFUzZQnggtv4g0CsExa-ayBmQqe80VwC13pQ… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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