Freesurfer

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30080 discussions

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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Open Position: Postdoc or PhD Student for Deep Learning based Lesion Recognition in human MRI
by Dr. rer. nat. Johannes Jungilligens 11 Jun '21

11 Jun '21

External Email - Use Caution *Postdoc or PhD Student for Deep Learning based Lesion Recognition in human MRI* available from July 1st, 2021, or later. The position will be embedded in a three-year project within the Human Centered AI Network (HUMAINE) at Ruhr-University Bochum (RUB), Germany. The highly interdisciplinary project deals with the identification and characterization of epilepsy-causing lesions in MRI images of the brain and their discrimination from non-epileptogenic lesions. The project is conducted at the epilepsy center of the university medical center Knappschaftskrankenhaus (Ruhr-Epileptology, Jörg Wellmer) in close collaboration with the Bioinformatics group at the Center for Protein Diagnostics RUB (Axel Mosig). The applicant should hold a degree in computer science, physics, or comparable studies and have experience along with profound theoretical and practical knowledge of deep learning in the context of three-dimensional medical imaging, in particular using state-of-the-art frameworks such as tensorflow of pyTorch. We offer an inspiring working environment in well-established interdisciplinary structures, providing state-of-the-art IT infrastructure in a highly dynamic interdisciplinary setting with project partners covering the whole range between medicine, machine learning, sociology, and business. The salary is that of a full-position scientist according to German payment standards. For further information and application, feel free to contact Jörg Wellmer ( Joerg.Wellmer(a)kk-bochum.de) and Axel Mosig (axel.mosig(a)rub.de)

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