External Email - Use Caution Hi Doug
I tried that as well but getting the same error as with --replace 29 3. ERROR: CTABpruneCTab(): ctab does not have segid 2 Thanks, julie On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. < dgr...@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. < > dgr...@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.ot...@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 >>> >>> 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. Any unauthorized use of >>> the information contained in this message is prohibited. >>> >>> >>> ___ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <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. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at*MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> http://secure-web.cisco.com/1lIsv08dXGf3m15hZry1rP2JzVH9P4XD4agmondF6b6d42rPxDjRxdzDoIDxjzOXyV6HqG2XPvgw0tceT4WNFatDoS9m3Pn2bPFGGgSy5hWOx89Vy5iOY5oA1p82eHHX0WRe_omnRPzh_miuLPWGbDSPSCvAAmXFiiOkTFERxwkV_dRO0LcvFj1auZ9hv0PLaII9MbqPS49bgW7gVczQgq8m2aDO7BPY3dwZtHHjtQDj43D_Bpb8c5OFi0N9Qk1l36rfpuExfXdlOi8CbpK_K1g/http%3A%2F%2Fwww.partners.org%2Fcomplianceline >>> >>> <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1M09yOMvL3bxuafFPhziW3AuSb0I6Z72Qov33u26r4dn33dQ3_VSrjfsn_a-YiZptxLG3EMDxSuoSvKETdQslM6ACw2z0tzhO2HI9gsWpoWhxGrBnkwlzPldv1JUOkE6Joog4JviL72Mu-L5IlshSIm8hgs-LFZAoKOiaiYhpRb2R6LhEw31ct--bG2jtxUqnHhBq0c8JtpYZ9X3m1U3mSQqpQLCxw0GzTxc4JtiQ/http%3A%2F%2Fwww.partners.org%2Fcomplianceline> >>> . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>> 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://secure-web.cisco.com/1hTIE4J4o9ru5GbW02rRzpqE0ElIuKqz90Py4oHrzoxUal0yxxVmSYagA4io8okeA6Ia-aXfV8O2oiAeImWkmU5Lk_jlqPYF72kguI8aTyxs0UJf9dAmZ0KcrM3MdJYbUrErvMztEx-VK8l_5VhneQUwcgdNOy_mhBhSkVvE0XsUDIpQz5tMAL8z1_S6OFkyFLaGhEgKgJFmoCrXoVZGf3hGG66pu2Zp7kO4Z796LH5QMbOtxHDp2-1ue4NmvDI4y-SNKnwnT4t0e9-pcyGCLpA/https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2 >>> >>> <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 >>> > *MailScanner has detected a possible fraud attempt from >>> > "secure-web.cisco.com" claiming to be* >>> > https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> > >>> > <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4--IR51ceGnrKkJGuKZyH2-xBD7NPg7YRk5xGt356FBgnh7s_NJvPNx6DXTeby31cgFfAZmjeY1zqLTmBgNiqrJ3vVoqcISrtcE4ccBmMdjnl0GKfC9gAQtaivKH5JV92lLPvCWunFHfJNBtV0S44Irx6oEpu1M-vnv0kROAmW7caS0pTfcXiWbZrGpiPdCLwyCGn0v2lWHWA8XN8HuwghV0gpxkcOV3twOkBsXREMQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR centergr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://secure-web.cisco.com/18hglveD2QhtSJ7bQFM9F3sXBln9p2f7eLtue0lnyouc5FBCs3HKarbm4lqp9n0Kf68yi6AZQXJyjNzgMIAN0xylcV-XYopkxaAWO50uaReuRvcauccYLGK6RvKxXYuqCwFRGLpdH6NSq5GqKxqsnUw3-iWKeLZguuD1GHQywuNyyCuE_T6yCJ5j-2Fk4U_CMck4EMDOkgD60HaUUaviGpr79mILr5gDtbwL49-MByPIqFZPm2htxVjzwNoSD1DMKfspVzhxUsfs-Q_mQqr4D3Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting> >>> FileDrop: *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1hTIE4J4o9ru5GbW02rRzpqE0ElIuKqz90Py4oHrzoxUal0yxxVmSYagA4io8okeA6Ia-aXfV8O2oiAeImWkmU5Lk_jlqPYF72kguI8aTyxs0UJf9dAmZ0KcrM3MdJYbUrErvMztEx-VK8l_5VhneQUwcgdNOy_mhBhSkVvE0XsUDIpQz5tMAL8z1_S6OFkyFLaGhEgKgJFmoCrXoVZGf3hGG66pu2Zp7kO4Z796LH5QMbOtxHDp2-1ue4NmvDI4y-SNKnwnT4t0e9-pcyGCLpA/https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2 >>> >>> <https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r61iT8Z2j9As6vvtakVyyW6C_EaPlVDGPsQrYaiBRU-MJ0Kd8bmcgwZb-AqT-JqQ3paxz8c8Q11n6VMbZsqwkhzjOjMZgtxJpp1DZiGIhWQagcZ_2l7xa9T1SmSeTqTvm75FEJSnbBgClBdvllPCyXVePyPDjUMNed3LQxEs_-XXf64uPIY4u2Ah7TVn-fLpf3MbLAIdL0tLIdW3GWFTjrD7SCSOXJNAeQKOnrztLkQ/https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2>*MailScanner >>> has detected a possible fraud attempt from "secure-web.cisco.com" claiming >>> to be* >>> http://secure-web.cisco.com/1afSqYPSIirqiNdqRn_fxtobSOVV12ByjyxNlb1xtfGnoZICFVWuGMCvCFeqN9qZQeKivpUYYfTC2jxYVD5NPmgDqNUFCGGL84fpUeJXo8DvDjX2ict1TJVOCSgoMhgWWzY3mvUbZsEecQqVcjyUJYUAvdvS39uWLElhzKFJyavlKeG-Qu-FS51r502nDS4alKNC4yc29RNW7AQkkceoQP1LS7DLmkuOZs6U_SID_6PkBlGv9XvqjMhpZSCawjKO9zu3Rf-4dHsfyG4DqnKGVGA/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html >>> >>> <http://secure-web.cisco.com/19vdC8-giAFd6ifd70PmXkEzKNFxO_PL9uIhgUKTBRjgXJMisc-gVrzi8q2s1HSBsYuZX7DTjBc8Ji064CHh0GaK9qFMUuctEsKk04LHlTToQsfhDHP8psC8vfssvpuLr1N724tk_hbGQbfCaBJLqjC1QRP8eYNpgA-71hpSN6oy4Hm8p-86szGoDB8Ws8z4zC2lR3ptjU8_l2llkaOE_4yEAQj95FTelB_IuBZSUMgAKUUxCFNOItdU82qLeUoYgfgMdZ9eHzVg95uKk4z6SgQ/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html> >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <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. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at*MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> http://secure-web.cisco.com/1lIsv08dXGf3m15hZry1rP2JzVH9P4XD4agmondF6b6d42rPxDjRxdzDoIDxjzOXyV6HqG2XPvgw0tceT4WNFatDoS9m3Pn2bPFGGgSy5hWOx89Vy5iOY5oA1p82eHHX0WRe_omnRPzh_miuLPWGbDSPSCvAAmXFiiOkTFERxwkV_dRO0LcvFj1auZ9hv0PLaII9MbqPS49bgW7gVczQgq8m2aDO7BPY3dwZtHHjtQDj43D_Bpb8c5OFi0N9Qk1l36rfpuExfXdlOi8CbpK_K1g/http%3A%2F%2Fwww.partners.org%2Fcomplianceline >>> >>> <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1M09yOMvL3bxuafFPhziW3AuSb0I6Z72Qov33u26r4dn33dQ3_VSrjfsn_a-YiZptxLG3EMDxSuoSvKETdQslM6ACw2z0tzhO2HI9gsWpoWhxGrBnkwlzPldv1JUOkE6Joog4JviL72Mu-L5IlshSIm8hgs-LFZAoKOiaiYhpRb2R6LhEw31ct--bG2jtxUqnHhBq0c8JtpYZ9X3m1U3mSQqpQLCxw0GzTxc4JtiQ/http%3A%2F%2Fwww.partners.org%2Fcomplianceline> >>> . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>> >>> 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 listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <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. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at*MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> http://secure-web.cisco.com/1lIsv08dXGf3m15hZry1rP2JzVH9P4XD4agmondF6b6d42rPxDjRxdzDoIDxjzOXyV6HqG2XPvgw0tceT4WNFatDoS9m3Pn2bPFGGgSy5hWOx89Vy5iOY5oA1p82eHHX0WRe_omnRPzh_miuLPWGbDSPSCvAAmXFiiOkTFERxwkV_dRO0LcvFj1auZ9hv0PLaII9MbqPS49bgW7gVczQgq8m2aDO7BPY3dwZtHHjtQDj43D_Bpb8c5OFi0N9Qk1l36rfpuExfXdlOi8CbpK_K1g/http%3A%2F%2Fwww.partners.org%2Fcomplianceline >>> >>> <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1M09yOMvL3bxuafFPhziW3AuSb0I6Z72Qov33u26r4dn33dQ3_VSrjfsn_a-YiZptxLG3EMDxSuoSvKETdQslM6ACw2z0tzhO2HI9gsWpoWhxGrBnkwlzPldv1JUOkE6Joog4JviL72Mu-L5IlshSIm8hgs-LFZAoKOiaiYhpRb2R6LhEw31ct--bG2jtxUqnHhBq0c8JtpYZ9X3m1U3mSQqpQLCxw0GzTxc4JtiQ/http%3A%2F%2Fwww.partners.org%2Fcomplianceline> >>> . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>> 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. >>> >>> Best regards, >>> >>> Donatas >>> >>> >>> >>> ___ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4--IR51ceGnrKkJGuKZyH2-xBD7NPg7YRk5xGt356FBgnh7s_NJvPNx6DXTeby31cgFfAZmjeY1zqLTmBgNiqrJ3vVoqcISrtcE4ccBmMdjnl0GKfC9gAQtaivKH5JV92lLPvCWunFHfJNBtV0S44Irx6oEpu1M-vnv0kROAmW7caS0pTfcXiWbZrGpiPdCLwyCGn0v2lWHWA8XN8HuwghV0gpxkcOV3twOkBsXREMQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> >>> ___ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <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. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at*MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> http://secure-web.cisco.com/1lIsv08dXGf3m15hZry1rP2JzVH9P4XD4agmondF6b6d42rPxDjRxdzDoIDxjzOXyV6HqG2XPvgw0tceT4WNFatDoS9m3Pn2bPFGGgSy5hWOx89Vy5iOY5oA1p82eHHX0WRe_omnRPzh_miuLPWGbDSPSCvAAmXFiiOkTFERxwkV_dRO0LcvFj1auZ9hv0PLaII9MbqPS49bgW7gVczQgq8m2aDO7BPY3dwZtHHjtQDj43D_Bpb8c5OFi0N9Qk1l36rfpuExfXdlOi8CbpK_K1g/http%3A%2F%2Fwww.partners.org%2Fcomplianceline >>> >>> <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1M09yOMvL3bxuafFPhziW3AuSb0I6Z72Qov33u26r4dn33dQ3_VSrjfsn_a-YiZptxLG3EMDxSuoSvKETdQslM6ACw2z0tzhO2HI9gsWpoWhxGrBnkwlzPldv1JUOkE6Joog4JviL72Mu-L5IlshSIm8hgs-LFZAoKOiaiYhpRb2R6LhEw31ct--bG2jtxUqnHhBq0c8JtpYZ9X3m1U3mSQqpQLCxw0GzTxc4JtiQ/http%3A%2F%2Fwww.partners.org%2Fcomplianceline> >>> . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>> [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. >>> >>> >>> >>> Best regards, >>> >>> Donatas >>> ___ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >>> be* >>> https://secure-web.cisco.com/1XKlN8n_R0qs3AtLIVv_QFpCDEofONu4yvZY36J4mYPZY3ZYice0CWktnfMGYBZNs4uJTDFUBgtvqTCPTla1bUHMJcf3GHy85T2-hl-wT3cvaLgywNODOV9CuUUBB4kdwAfBd5-6FeccmAvlFD22X9ONGtXsEVmcrHs0BdWar0kq47_l_aXppXthlaOkKFYPmNyHsV0jq2gqyAp4XcP1_VkOQa6tk6F7HXJZE47JGGllJUS3XaOY0XlKPAxcFtECUotCuJZ9Jle7RpW8L8gfRmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <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. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at*MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> http://secure-web.cisco.com/1lIsv08dXGf3m15hZry1rP2JzVH9P4XD4agmondF6b6d42rPxDjRxdzDoIDxjzOXyV6HqG2XPvgw0tceT4WNFatDoS9m3Pn2bPFGGgSy5hWOx89Vy5iOY5oA1p82eHHX0WRe_omnRPzh_miuLPWGbDSPSCvAAmXFiiOkTFERxwkV_dRO0LcvFj1auZ9hv0PLaII9MbqPS49bgW7gVczQgq8m2aDO7BPY3dwZtHHjtQDj43D_Bpb8c5OFi0N9Qk1l36rfpuExfXdlOi8CbpK_K1g/http%3A%2F%2Fwww.partners.org%2Fcomplianceline >>> >>> <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1M09yOMvL3bxuafFPhziW3AuSb0I6Z72Qov33u26r4dn33dQ3_VSrjfsn_a-YiZptxLG3EMDxSuoSvKETdQslM6ACw2z0tzhO2HI9gsWpoWhxGrBnkwlzPldv1JUOkE6Joog4JviL72Mu-L5IlshSIm8hgs-LFZAoKOiaiYhpRb2R6LhEw31ct--bG2jtxUqnHhBq0c8JtpYZ9X3m1U3mSQqpQLCxw0GzTxc4JtiQ/http%3A%2F%2Fwww.partners.org%2Fcomplianceline> >>> . 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