External Email - Use Caution Hi Doug,
Did you have a chance to look at this subject ? Thanks a lot, Julie ---------- Forwarded message --------- From: Julie Ottoy <julie.jj.ot...@gmail.com> Date: Thu, 18 Mar 2021 at 13:08 Subject: Re: [Freesurfer] Failed tissue type check {Disarmed} To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Hi Doug I upload the files on the server, see subject_ottoy.tar.gz thanks a lot! Julie On Tue, 16 Mar 2021 at 12:03, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > 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.ot...@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.ot...@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 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2VSz5jSBD9SbRbwnyLf2Vt9hRpIi52nRa-_btbxLc4MfsOrL4o8Kn5ClTo8UlgAd5vZZlh8MIQUoxHBs2HEEzsjry2zpA7adjkLUEdgkQw8S5xXALCxmCk45_8RH-qf3iunCvn6RgbRnd2WaID_yXhp605fsbF-JCEEkNOF5A1rkSKz33PwqOHU_oEWgQBsGlu-hxFiuI4SHKtt6jscjuC0F2-PVQH6cOB570hs3iQ/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/1eGgq3MtUZinN6YC13LiaDErXWJN9vgi9QwYQxtVWBl6EaVgRT4NrdKSi46UgZcb6hhtMvkjdq-cQq5LWSbzTH3M2A9LBp7Z4yiqSAY8i-hT3-1BnbH7dGxfSrSUMm849trLc0MRzFLlwZ9-jfhtOernnKbo90fzgh1t4xoRdEkchUhZU9M4NIng7039nltyD57-PxCxxn9UpKZbDSfq8Tge0WQeFOr2PTkJYaAZLu0Fjn0TqJ8VciAfNlpQZJxKHunXIJrKXTdSLUH88zbfHxQ/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1eGgq3MtUZinN6YC13LiaDErXWJN9vgi9QwYQxtVWBl6EaVgRT4NrdKSi46UgZcb6hhtMvkjdq-cQq5LWSbzTH3M2A9LBp7Z4yiqSAY8i-hT3-1BnbH7dGxfSrSUMm849trLc0MRzFLlwZ9-jfhtOernnKbo90fzgh1t4xoRdEkchUhZU9M4NIng7039nltyD57-PxCxxn9UpKZbDSfq8Tge0WQeFOr2PTkJYaAZLu0Fjn0TqJ8VciAfNlpQZJxKHunXIJrKXTdSLUH88zbfHxQ/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/1En2sExPLORX4J1w9LZmBmOFgR3GA3uFmBVMOMf2e7NMCyvxMjSV_M88h8Z1Hu_SRhIdA654U6fK2505TXNsNXNLE3pU9npMrUzkP8lugETjtnYXRuBP46BA8-LgSBOusyMCeDwkA8dgQquZRNVUbat8QyuVGRROlTqXJigC9uBGxZnufrVP-YNP9eZGNq5MasJvzgMSb2ivcPKAyKy6xVWIscuh4kut5spwnbz7S3lGQcSM_B9Zzo5-8KgZkJEoeYGPmua_dUGkdX_MEQ6KmqQ/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2VSz5jSBD9SbRbwnyLf2Vt9hRpIi52nRa-_btbxLc4MfsOrL4o8Kn5ClTo8UlgAd5vZZlh8MIQUoxHBs2HEEzsjry2zpA7adjkLUEdgkQw8S5xXALCxmCk45_8RH-qf3iunCvn6RgbRnd2WaID_yXhp605fsbF-JCEEkNOF5A1rkSKz33PwqOHU_oEWgQBsGlu-hxFiuI4SHKtt6jscjuC0F2-PVQH6cOB570hs3iQ/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2VSz5jSBD9SbRbwnyLf2Vt9hRpIi52nRa-_btbxLc4MfsOrL4o8Kn5ClTo8UlgAd5vZZlh8MIQUoxHBs2HEEzsjry2zpA7adjkLUEdgkQw8S5xXALCxmCk45_8RH-qf3iunCvn6RgbRnd2WaID_yXhp605fsbF-JCEEkNOF5A1rkSKz33PwqOHU_oEWgQBsGlu-hxFiuI4SHKtt6jscjuC0F2-PVQH6cOB570hs3iQ/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2VSz5jSBD9SbRbwnyLf2Vt9hRpIi52nRa-_btbxLc4MfsOrL4o8Kn5ClTo8UlgAd5vZZlh8MIQUoxHBs2HEEzsjry2zpA7adjkLUEdgkQw8S5xXALCxmCk45_8RH-qf3iunCvn6RgbRnd2WaID_yXhp605fsbF-JCEEkNOF5A1rkSKz33PwqOHU_oEWgQBsGlu-hxFiuI4SHKtt6jscjuC0F2-PVQH6cOB570hs3iQ/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/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/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2VSz5jSBD9SbRbwnyLf2Vt9hRpIi52nRa-_btbxLc4MfsOrL4o8Kn5ClTo8UlgAd5vZZlh8MIQUoxHBs2HEEzsjry2zpA7adjkLUEdgkQw8S5xXALCxmCk45_8RH-qf3iunCvn6RgbRnd2WaID_yXhp605fsbF-JCEEkNOF5A1rkSKz33PwqOHU_oEWgQBsGlu-hxFiuI4SHKtt6jscjuC0F2-PVQH6cOB570hs3iQ/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 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>>> <https://secure-web.cisco.com/14NSCNEWI-E5xedPGXzQlT7gdo_k2vDQZC-njeqsKjvbqvQeIjJt1ay3FZW6MKrMx1pUBnSHvCzaAd4XfgvhOGKfzo2aWmS20qTTCkZ2B8VSFrwxmo_207d1PC0VzB144nh-BBhuygXrnwvNsw04HnzZA_dure7Qp3eqzDTOuKrQ_ju-mBCM0XTwbOj1McVLC4giooX3R2yD4RkggeL1YFFEKwq6nLB4sGdMk0xO5_PghclJ4T0Imsk6A6hP9aHtjanXvcvRhxvdnJZxbc0Q1VQ/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> >>>>> <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJqmPVauMgye27XenRCyW2RS0NRxLkcR1OoNBeHGUfzDoIp4j6b42zzPwQevNYKvmMb9nOxzG7B4sqbSRmGPPSkC-PWiTeMTc30aZjdjf857XnvJFeZuxSKRNefHfNFyZcQmwZqPAhPL5d1nOXJYwO429ya5ccWZe3Gbe_y0oLS5xGqhzJAXI7qCHxRjnCxI3nRz7nIkN3dQIDfurSNEi1EK1rmdSSlLc99qzHa8kP0w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJqmPVauMgye27XenRCyW2RS0NRxLkcR1OoNBeHGUfzDoIp4j6b42zzPwQevNYKvmMb9nOxzG7B4sqbSRmGPPSkC-PWiTeMTc30aZjdjf857XnvJFeZuxSKRNefHfNFyZcQmwZqPAhPL5d1nOXJYwO429ya5ccWZe3Gbe_y0oLS5xGqhzJAXI7qCHxRjnCxI3nRz7nIkN3dQIDfurSNEi1EK1rmdSSlLc99qzHa8kP0w/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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/1DOc6HK09tTHDCTRe3zaykFn4umMUwn8-y6MGj0gOXqv_QC_FdHo-H2qwQCdtFFPBesqq7LAYVY5yy_EXnXRoIWBv6W9nN_gMva1jUAnkJKXDH0hMzxNmLZ3-v7Wo0rdjbz9rGFbrKbL3nHcEzGn021qGNc9wmlCesMHhK8c3x9FjHjeWDjHF3HKpTVbHwu4IiP5VGKvtxH-uH1a9M9GQfi1CCBxm_rc1r8H9kyZWerEsnN2muYgViVRCsPDYMXh2QN0_qICtbfYwAqLIC_BEgQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>>> >>>> >>>> _______________________________________________ >>>> 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> <https://secure-web.cisco.com/1DOc6HK09tTHDCTRe3zaykFn4umMUwn8-y6MGj0gOXqv_QC_FdHo-H2qwQCdtFFPBesqq7LAYVY5yy_EXnXRoIWBv6W9nN_gMva1jUAnkJKXDH0hMzxNmLZ3-v7Wo0rdjbz9rGFbrKbL3nHcEzGn021qGNc9wmlCesMHhK8c3x9FjHjeWDjHF3HKpTVbHwu4IiP5VGKvtxH-uH1a9M9GQfi1CCBxm_rc1r8H9kyZWerEsnN2muYgViVRCsPDYMXh2QN0_qICtbfYwAqLIC_BEgQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6lQYtOpyaUsD7xusnX7vhIg8mBTG2hQuHMlARYDEQLc7fxcAaRPcIsL4K-Cd314el-NXoLBCERR8sg1u0NuTU62rJ8qox8mz1CYvFlw5d9TDfyYLEJxAfZdZFBcsYrARxIQePsr5SBW_DF8sP_kVR6P2OXrKHXcYCgktzfDOj0aVOZbCQ2m01Y9qRAEuFFD_EEeGMyjjMi8QiyTnNsBhE7M7TNUtR4KGEd1hi7gIug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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