Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] “Illegal instruction (core dumped)” in mri_synthseg and mri_synthsr
by fsbuild 01 Apr '22

01 Apr '22

External Email - Use Caution Hello Gonzalo, We’re aware that some binaries will not run on older Intel processors that do not support AVX instructions.  You could try running it on a different machine with a newer intel CPU.  We’ve also has some reports about this on Apple hardware with M1 processors and are looking into it. - R. On Apr 1, 2022, at 17:00, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:       External Email - Use Caution        Hi: I tried to use mri_synthseg and mri_synthsr commands, but I got theerror message "Illegal instruction (core dumped)". Any solution? Ihave the March 31st, 2022 version. Sincerely,Gonzalo Rojas CostaDepartment of RadiologyClínica las CondesLo Fontecilla 441, Las Condes, Santiago, Chile.Tel: 56-2-2105170Cel: 56-9-97771785https://secure-web.cisco.com/1A3UQ11G-wOv-3pW2zSaWtZKG8SS328lgaqQXucSvEjh6odB-KDmWxYXm4OCFP3VTPEYF9hixnewYKSlG7U33uk7GWkTJW6hJiGRkhdV_vDr7AMoQ_fDtCehpAMSERscngsF_9sVywi05i9ZSVyFj92rhbO080hMC0i6fHZ_MZg69OILUh5UpP4_dEkx1qnSe2RZRG9FibNQxe9UsmqWHfXxwUZplkELriSfTXkcGJJBKRE0sIKnqxcf9cJaaCAIILk8QvhuDqeQXsDu_ZEj0ydi__kwRkHsgw9bZW2-o-G4eMML6GiZG0eV9lroWlpGJPlz_nblO3Gn1tZkXPPRe-g/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oAAAAJhttps://secure-web.cisco.com/1mvpNMRQKSP8FkYyfvVpb7eLS9lj8kZfszgSu9oRJQ8X5gT1o5EbOPN9_w0I95lz3bmOOhFKTa2yoVqxi7B3ZxSiDoHdeWmAqnJ6H2C4zZ0V-Dryb5Fpf5HJAloFFnAPsltFLGzloThFZvs6eFlGeVt7cSS1vWQsIhhM1FylufIpPjPqlNUy1L4AaJ6HlQtupYff3l2933LsgOOn6hPtplYjxT35EZg2jWOhSoBoJqYbI6T5McFyGjNG6_xmplW_nWwnr2nGkwIP7R2THKOSbB2oi_XpvElIQbTLyxgEOSjJaSbVmrbfjwXlAdkK5xx5iyvuPMc7Ki0qOdzWHpNM0Ew/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2https://secure-web.cisco.com/1BSQzDFZczyH2KnRdF2ICVDpUxz6g0ttdU0u-j9PVXo7bIp_PAiaidUZgqXnba0vu5Bcu80MTlDSLj_H7drSSmjw9o-ApoFWbGvavQaIPYZkWqEeyYHXffZDlBqPAfGOKiijJqECUGZQ0ZkgMjioihhpc_46unYRzJwP_Olaq_uOLxoBnFiOk7RIEOQOrq4m6ogPai73zS4t5-NWaw-Mn-m-7R5KlfS9by8_FWZHpa8Er7-QUKcjE38ltkwFIVoarGW9OvPw0N-crWzU8IYfcTPNe5bDV_hl0-6p7OS4tpeaMilAitHaZVfbxHEjfdo0qXAT3CbbKH9FEWORrybZ44Q/https%3A%2F%2Fcvn.fecyt.es%2F0000-0002-6228-2678http://secure-web.cisco.com/1dOFt7henxwABk7hXay_AiRKApZWkzldFKpSeFu7YZA9mXuuq9U_88R1YuXngvPpHdu4VYrPFXW8qpV_t3rjlxPDrWmJNKmo7DIqMAcaKYwVd34QHt8Vu2frhBEQ5zp0hhEKyySjNS26mVbfna1FwRR2qFoO4GLoa0O-CUfmtFcpmQp1ZS5tB3IIIooNFaP9ioUIuL6frrXyXTu8HtC7ofXbWJekLulscwlodKoWS9-0rO63GYRLbZPq7ezoZNSITVOB6XKri_qCiUi8hy6OQd2arca-LWXt0BwR65j3RHAX2DYtTHt-hFCsLj9gxEGZppeokmXXZGI__MKC2zTaPkw/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013https://secure-web.cisco.com/1Th1b2nsH7DOoOS75firwrxXGmPTRXXCJK7nGZMWtY8MELWqNmHiJIS9tMuuGkwnYTZ9aJ15O9a5OeCMYTkOBAPIwIDNZjyO4qlCxeP18bVZa0AvP26wB6Qkdew8E7SeIKlwzJWNlh6zOfjaJO3m5Z-4JtKJdxdQGlOCiylUc1b9uoVLu836jxV38np5BFFUBTUXiqXiPHMJ4c-zCdHzMc2cH0X2THYKZG7S39ZW0lJvDZHwg7dYeDZZ6o4Xx08zkRjVR00HM35JJbEavZAQ2orYZuhSCzBQl4JG4DH-xQwa1qsm_N_RKSzTcQ26dMv7fiNbb3_KBGtQBzOCM8yU5aw/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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“Illegal instruction (core dumped)” in mri_synthseg and mri_synthsr
by Gonzalo Rojas Costa 01 Apr '22

01 Apr '22

External Email - Use Caution Hi: I tried to use mri_synthseg and mri_synthsr commands, but I got the error message "Illegal instruction (core dumped)". Any solution? I have the March 31st, 2022 version. Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1A3UQ11G-wOv-3pW2zSaWtZKG8SS328lgaqQXucSvEjh6o… https://secure-web.cisco.com/1mvpNMRQKSP8FkYyfvVpb7eLS9lj8kZfszgSu9oRJQ8X5g… https://secure-web.cisco.com/1BSQzDFZczyH2KnRdF2ICVDpUxz6g0ttdU0u-j9PVXo7bI… http://secure-web.cisco.com/1dOFt7henxwABk7hXay_AiRKApZWkzldFKpSeFu7YZA9mXu… https://secure-web.cisco.com/1Th1b2nsH7DOoOS75firwrxXGmPTRXXCJK7nGZMWtY8MEL…

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Re: [Freesurfer] Password for virtual machine
by fsbuild 01 Apr '22

01 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 1, 2022, at 13:03, Ogier, Stephen E. (Assoc) <stephen.ogier(a)nist.gov> wrote:        External Email - Use Caution        Hi, I’m getting started with FreeSurfer, and I was wondering if I could be sent the passcode to unzip the virtual machine? Thanks,Stephen Stephen Ogier, PhDPostdoctoral Associate, Magnetic Imaging Group, Applied Physics DivisionNational Institute of Standards and Technology_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Seeking beta testers for new Freesurfer help forum
by Sennott, Liam Ricker 01 Apr '22

01 Apr '22

Hello, FreeSurfer community, The FreeSurfer administrative team is working on transitioning the current FreeSurfer mailing list infrastructure to a new, more user-friendly platform called Discourse. We’re still finalizing the website, so we’re looking for potential beta testers for this new platform. As a beta tester, you will post your questions to Discourse and interact with the FreeSurfer staff in discussion board format. Please email lsennott(a)mgh.harvard.edu<mailto:lsennott@mgh.harvard.edu> if you are interested in helping us test this new system! Thank you, Liam Sennott FreeSurfer Admin

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Password for virtual machine
by Ogier, Stephen E. (Assoc) 01 Apr '22

01 Apr '22

External Email - Use Caution Hi, I'm getting started with FreeSurfer, and I was wondering if I could be sent the passcode to unzip the virtual machine? Thanks, Stephen Stephen Ogier, PhD Postdoctoral Associate, Magnetic Imaging Group, Applied Physics Division National Institute of Standards and Technology

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license text
by krystaly 01 Apr '22

01 Apr '22

External Email - Use Caution Dear Free Surfer experts, I just downloaded the newest version of Free Surfer. The system says FS_LICENSE=/home/developer/license.txt set in /home/developer/.bashrc does not point to a freesurfer license. Freeview will not run w/o a license - edit FS_LICENSE to point to your license file. Would you please send the license key to me? Thanks! Best regards, Krystal

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WM error near the right putamen
by Gabor Perlaki 01 Apr '22

01 Apr '22

External Email - Use Caution Dear all, fswiki suggests that " There are regions where the surfaces are not intended to be accurate that you should be aware of: Areas around the hippocampus and amygdala. " I also found inaccuracy of the WM surface near the putamen and accumbens regions. WM surface goes into the putamen (please see the attached picture). Do I need to fix this error or is it normal? Are the thickness of ctx-rh-medialorbitofrontal and the volume of right putamen valid in this case? Thank you in advance, Gabor

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Re: [Freesurfer] illegal instruction 4 Mac M1
by fsbuild 31 Mar '22

31 Mar '22

External Email - Use Caution Hello Miriam, I can reproduce your error running mri_sclimbic_seg on an M1 Mac running MacOS BigSur with the latest freesurfer development build.  We will look into this and see what can be done. - R. On Mar 31, 2022, at 16:14, Miriam Taza <miriam.taza(a)mail.mcgill.ca> wrote:        External Email - Use Caution        Hello,I am trying to run mri_sclimbic_seg command using dev version of freesurfer on my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal instruction: 4 (here is the output)/Applications/freesurfer/python/scripts/mri_sclimbic_seg --i Desktop/doc/corlab/sub-121123/anat/sub-121123_T1w.nii.gz --o Desktop/doc/derivatives/MT/corlab/sclimbic_output/sub-121123/anat/rois/sub-121123_atlas-sclimbic_dseg.niiExcluding seg [853]Using CPUIllegal instruction: 4I am very new to coding and first time using freesurfer. Unfortunately, my lab mates have not had a similar problem as they all have intel-based macs. Thanks!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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illegal instruction 4 Mac M1
by Miriam Taza 31 Mar '22

31 Mar '22

External Email - Use Caution Hello, I am trying to run mri_sclimbic_seg command using dev version of freesurfer on my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal instruction: 4 (here is the output) /Applications/freesurfer/python/scripts/mri_sclimbic_seg --i Desktop/doc/corlab/sub-121123/anat/sub-121123_T1w.nii.gz --o Desktop/doc/derivatives/MT/corlab/sclimbic_output/sub-121123/anat/rois/sub-121123_atlas-sclimbic_dseg.nii Excluding seg [853] Using CPU Illegal instruction: 4 I am very new to coding and first time using freesurfer. Unfortunately, my lab mates have not had a similar problem as they all have intel-based macs. Thanks!

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Tracula fsl commands fail in Freesurfer docker
by Clément Nicolas Graffard 31 Mar '22

31 Mar '22

External Email - Use Caution Hi, I am trying to use tracula within the freesurfer docker (freesurfer:7.2.0) but some commands related to fsl fail because the fsl script is not found. For example, within the trac-preproc command, the subcommand bet /input/inputData/sub-010017/dmri/lowb.nii.gz /input/inputData/sub-010017/dmri/lowb_brain.nii.gz -m -f 0.3 is launched but this script is named bet.fsl instead of just bet in the folder /usr/local/freesurfer/bin inside the docker. This causes the command to fail. Have I missed some initialization steps ? Many thanks, Clément Nicolas--Graffard

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