16 Mar
2021
16 Mar
'21
12:02 p.m.
I don't know. Can you upload the data so I can take a look? Instructions are below. I'd need both the anatomical data (output of recon-all) and input.nii.gz and PET.lta
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 3/8/2021 11:47 AM, Julie Ottoy wrote:
External Email - Use Caution
Hi Doug,
Any other suggestions I could try? It seems to be only an issue with the non-pvc data.
Thanks Julie
On Tue, 2 Feb 2021 at 11:10, Julie Ottoy <julie.jj.ottoy@gmail.com mailto:julie.jj.ottoy@gmail.com> wrote:
Hi Doug, I tried these fixes but they still give me the error message below. I did replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab in the aux folder ? Thanks, Julie On Tue, 12 Jan 2021 at 10:37, Julie Ottoy <julie.jj.ottoy@gmail.com <mailto:julie.jj.ottoy@gmail.com>> wrote: Hi Doug I tried that as well but getting the same error as with --replace 29 3.ERROR: CTABpruneCTab(): ctab does not have segid 2Thanks, julie On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: Try using --replace 29 2 On 12/29/2020 12:48 PM, Julie Ottoy wrote:External Email - Use Caution Hi Doug Thanks for your reply. I tried both your suggestions, but it seems as though they both ran into an error. For your first suggestion, i.e. adding --replace 29 3 to the command line of gtmpvc, I get the error: Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz Loading seg ctab 057_S_5295re/mri/gtmseg.ctab Reading 057_S_5295re/mri/gtmseg.lta Replacing 19 Pruning ctab ERROR: CTABpruneCTab(): ctab does not have segid 3 For your second suggestion, i.e. I replaced the following line in the ctab: 29 Left-undetermined 135 206 235 0 -1 ==> replaced by: 29 Left-undetermined 135 206 235 0 3 I get the error: Computing Seg in input space Building GTM DoVoxFracCor=0 ERROR: creating region for nthseg=12, segid=29, Left-undetermined It may be that there are no voxels for this seg when mapped into the input space. Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the registration Build time 5.9690, err = 1 Thank you, Julie On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: You can use the fix from my previous email or you can add the following line any were into the gtmseg.ctab file: 29 Left-undetermined 135 206 235 0 3 On 12/18/2020 11:06 PM, Julie Ottoy wrote:External Email - Use Caution Sorry I would like to correct my previous post. The subject also failed with PVC. I see now that the issue is happening during the gtm seg stage where it gives the error: WARNING: segid 29 Left-undetermined tissue type is not set. For your information: I ran the standard FS and petsurfer pipeline as outlined on the wiki. I tried two gtm seg commands: gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm --subseg-cblum-wm Thank you for your help, Julie On Fri, 18 Dec 2020 at 00:09, Julie Ottoy <julie.jj.ottoy@gmail.com <mailto:julie.jj.ottoy@gmail.com>> wrote: External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got the following error in only one of my subjects. When I ran the same subject with PVC and specified psf, it did run fine. $Id: mri_gtmpvc.c,- setenv - cd - mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o /gtmnopvc.output.ceregrey --rescale 8 47 sysname Linux hostname - machine - user - vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory /gtmnopvc.output.ceregrey Loading seg for gtm /ID/mri/gtmseg.mgz Loading seg ctab /ID/mri/gtmseg.ctab Reading /ID/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check Any suggestions would be appreciated! Thank you, Julie Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGDCYbw1nr7Bymh0JNbA3Nr4M_m3-TZzftvlgMiJh7YiC6aUDW4Al3Wj4Kuy-05sd4QjU4E_RzWvbOfb_BTd5VaY6BPCSTWz6zWkEU0xuqeLNwwPRnm1yANvQkKZrMAWw2Gw7xnEbbIx95EqXWVkcRYx-x2scLfRIy4vfC9Cwn0nm4LrwA7h_KSoSDmXwnNLtLoWCfmI3LlkSE6EtVO2bwfNHaGn2-d6rSu0cljwjoiw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg55983.html> 2017-11-25 <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8hnIkonyOL9FxrLNrp4Bj2WuN0PTQlUGm_PJQva6MLutv6BMWs-SO763W-gwW1nAT6N4vj217JzAEoSXtBbWL5JUyfL-O7BWGLfrj_ULjoLxBYnq2LcSNQgj9kva8w0E0bdnIFYTLoXYkJqjYbk7i-67h2LWjuOMCsdK3wV31zmywpixGXpXL85YXKxMmEETIQFPv9cZG3dAO4WLNFtjdVE1ZXCWD0o5zbpJqBYb5A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20171125%26o%3Dnewest%26f%3D1> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1> Douglas Greve <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV4jNz4fwyUMZPIMoCVdt9d_bUFEK6r8QndJ4GnxUzSJ5nFbTzLdgAE-xzB-cDHXFlDfjsbfBplG7gX0td56lZUCF6RZPQS86X8fx38fzgpoQ3ODino_OhrbrTLu_vxfi-hx0Kk2lh3HyNlKDTzyXnTgdkp2Aal7nkVZSeRuXTLXG3JF5hoKLtnmjEillAunhi3_Opx8m7CSxBHkkUEndRqMO7hLRg4xySjrREex2pQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BGreve%2522%26o%3Dnewest%26f%3D1> sorry, can you send me the details again? On 11/21/17 10:24 AM, Klein, Gregory wrote: Hello Donatas and Douglas, Did you ever find a cause and solution for this problem? I too occasionally get this error message, and cannot get the results of mri_gtmpvc for certain subjects. Any suggestions are welcome. Thanks, Greg -- Gregory Klein, PhD Principal Scientist, Biomarker Experimental Medicine Leader F. Hoffmann-La Roche Ltd. Bldg 01, Floor 16, N445 Grenazacherstrasse 170, 4070 Basel, Switzerland Mobile: +41 79 572 97 89 Office Phone: +41 61 682 07 59 email:gregory.kl...@roche.com <mailto:gregory.kl...@roche.com> Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City, AL7 1TW Registration No:100674 Confidentiality note: This message is intended for the use of the named recipient(s) only and may contain confidential and / or privileged information. If you are not the intended recipient, please contact the sender and delete this message. 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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1vNIDvkxU5C3l-uZggX6Oz-MWAWokjyVkJCUVlEhq9XKRou9eGi_P4M46IFpR1kCRi1EKRdkeOBFVqh_OIenn7kfRu7nFDiiYQiPVLDM9jIX0E7yXM3IE9wPxeznDUX86p23XfIyCQexiUW3J2iSp_8oimLG0_0MFG_52NsnSBnFqD95zM5NWkY9v-O4RpKVme7JotteOAkByGn4K2nOnNr29fs5plfI9d7x2djz-4Ue835833aaN9mt9CRa1r2Fs1RNS_IoGztF_ed1YuklfRQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50026.html> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1> Douglas N Greve <https://secure-web.cisco.com/1M-leUu9vjxLEhQIgnl6dfbF3d7ST4-ULxvVl3JoB7UDa6hmmV2wHG4MuoCNyc4UqAlh3sGuH6uPVehnQEBYfTZ4LfWBlxUL1C4y6nEYmFy5T7dRxmEjRRsskCH17qTU9FH2r8C1oRaLJeClsqrR1ShA5x1ISE7NIxSujmswYJ3ekqjXjMDBCY0hwrOIapdK6l18hl5CaQyuSq0dBeDzFYBuYXI_5YHApG1LcvLwprG2esMuzVfUP9g5XPYjOtIZKMyWa9Qg6N9UirE85iU7Y1A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN%2BGreve%2522%26o%3Dnewest%26f%3D1> Donatas, please remember to include previous correspondence so that we have everything in one email. Can you upload your freesurfer subject so that I can debug it further? upload to *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://gate.nmr.mgh.harvard.edu/filedrop2 <https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r61iT8Z2j9As6vvtakVyyW6C_EaPlVDGPsQrYaiBRU-MJ0Kd8bmcgwZb-AqT-JqQ3paxz8c8Q11n6VMbZsqwkhzjOjMZgtxJpp1DZiGIhWQagcZ_2l7xa9T1SmSeTqTvm75FEJSnbBgClBdvllPCyXVePyPDjUMNed3LQxEs_-XXf64uPIY4u2Ah7TVn-fLpf3MbLAIdL0tLIdW3GWFTjrD7SCSOXJNAeQKOnrztLkQ/https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2> On 11/09/2016 12:17 PM, Donatas Sederevicius wrote: > > I followed the processing workflow as described in PETSurfer wiki > and gtmseg.mgz was created using gtmseg script as described. I > ran this processing for over 100 subjects and only one has failed. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4--IR51ceGnrKkJGuKZyH2-xBD7NPg7YRk5xGt356FBgnh7s_NJvPNx6DXTeby31cgFfAZmjeY1zqLTmBgNiqrJ3vVoqcISrtcE4ccBmMdjnl0GKfC9gAQtaivKH5JV92lLPvCWunFHfJNBtV0S44Irx6oEpu1M-vnv0kROAmW7caS0pTfcXiWbZrGpiPdCLwyCGn0v2lWHWA8XN8HuwghV0gpxkcOV3twOkBsXREMQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> -- Douglas N. 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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1yv39xApOHJ3FS6xDcFycnMnbHtStZeNBiLl3QzfL8G4yuWqEeGFNYzyiQ33Ex-jCBtvZpJntii832vSyEk6xnN5IYHn5Srf9NA5CmqjyBtwhPnmxD_EsoeCGDEQW0hG5N_lDc1_iosQAG4k2qZ26umeGpKNIFRfSyM1nISnBVv4YTEoBjMQuweEKSCvNNFAmb-kDbh7mk-1AukTjK5yO0vqnjqi1AaUaaKOobt0r0FKGBTu7BfRTZB69YmwQv6W9R_6kXsldmgOPEtybOxAaig/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50024.html> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1> Donatas Sederevicius <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKlwU3UP25xnszjeeOUSTu4MAOtS07GmVt_x7VvtqpQoEAaS71PvpUOuuh2Jakccv8UApdQNTlnQdUnmjNnHmlGvLcg5IUijE2zaZXa9RYA8IDK_ah32UsYDVwGsJEoTOmWJw7z4syagjpNSb-3Md12zplk8Bk_VyLPOioLaFuLwkId-HkmUwYihnJP3FHPaoBvcC9nZcNp9aLf_oWZSt-7iToV4Zqf-IpHtddQTUy0A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Donatas%2BSederevicius%2522%26o%3Dnewest%26f%3D1> I followed the processing workflow as described in PETSurfer wiki and gtmseg.mgz was created using gtmseg script as described. I ran this processing for over 100 subjects and only one has failed. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4--IR51ceGnrKkJGuKZyH2-xBD7NPg7YRk5xGt356FBgnh7s_NJvPNx6DXTeby31cgFfAZmjeY1zqLTmBgNiqrJ3vVoqcISrtcE4ccBmMdjnl0GKfC9gAQtaivKH5JV92lLPvCWunFHfJNBtV0S44Irx6oEpu1M-vnv0kROAmW7caS0pTfcXiWbZrGpiPdCLwyCGn0v2lWHWA8XN8HuwghV0gpxkcOV3twOkBsXREMQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. 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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1vPxlf-9EcToYjQ2NcohNFPvheryGJhjZq4nxdkmbOKRg2omA5NkvMb0IblIRORZ1EoUy_uNZK78n0cJGkdzgNLgkKgbgrH6CwMUbGRrwurpX7PEF7YXvBsk3iQvBzt9B4WWXE2dF2qCPythWj_9RDNWO3rOCKW7J8-CFgKSLi4xVEHJtYnueAy-zQquTDSQGbXCyL47s3SpPzQZ6RX88M2Qf0zVigwKGWTeW9-6AOasIs7vnUUsbSasf1jSg1sKh9CeEzsLQstjOfhvzBEhNEg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50018.html> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1> Douglas Greve <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV4jNz4fwyUMZPIMoCVdt9d_bUFEK6r8QndJ4GnxUzSJ5nFbTzLdgAE-xzB-cDHXFlDfjsbfBplG7gX0td56lZUCF6RZPQS86X8fx38fzgpoQ3ODino_OhrbrTLu_vxfi-hx0Kk2lh3HyNlKDTzyXnTgdkp2Aal7nkVZSeRuXTLXG3JF5hoKLtnmjEillAunhi3_Opx8m7CSxBHkkUEndRqMO7hLRg4xySjrREex2pQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BGreve%2522%26o%3Dnewest%26f%3D1> Was gtmseg.mgz created with the gtmseg script? On 11/9/16 4:43 AM, Donatas Sederevicius wrote: Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. 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[Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1-KTvEDdAuFhtSF_p9XP0T2HYXV7p_VXGloR253IuV-slWQ30G_xnBl6OTD1xVEPHwQNraHUfoMiBn--OpbsCNvDeeg2yiiTFt_hNb9tG0rZs036N4J30PcPcxMbEeZJd8UKhBiWZIXXd3HJmU4EZDdWNusOUttj4KzgwnxJ_kQQSNjfFaZ3_2BQfSq-0GcHekQ-tjX1TcaUz5rYKp9tVt4pQNGbVmyUka548gRcJpGDFOGvz-1U_S6hDUcWvOKfrllmBmNeaQVTIHWSXmZZkhA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50013.html> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1> Donatas Sederevicius <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKlwU3UP25xnszjeeOUSTu4MAOtS07GmVt_x7VvtqpQoEAaS71PvpUOuuh2Jakccv8UApdQNTlnQdUnmjNnHmlGvLcg5IUijE2zaZXa9RYA8IDK_ah32UsYDVwGsJEoTOmWJw7z4syagjpNSb-3Md12zplk8Bk_VyLPOioLaFuLwkId-HkmUwYihnJP3FHPaoBvcC9nZcNp9aLf_oWZSt-7iToV4Zqf-IpHtddQTUy0A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Donatas%2BSederevicius%2522%26o%3Dnewest%26f%3D1> Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. 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