External Email - Use Caution
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
>>>>
>>>>
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>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has
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>>>> be*
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>>>>
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>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom it
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>>>> HelpLine at*MailScanner has detected a possible fraud attempt from
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>>>> http://secure-web.cisco.com/11kLega6aHANPuoB9nMBwLhMhSyMrekdgO1JGgNJnsRUb4j_L79yVzmlZlrYHbRifj9A1gpecgEss9vc-tsg0JLzEoZBQklMnXiB-f5NZehZByUaBLzHRtPekB6Nf6H0HYCK6RqBQPVIqbzVY20w8i906jiCKWlMlbgdByBL9MP6HC6koL45cmF2XRJnBkbD7gDHVzr3J0Wljf4tqYwuiLgay_O3Em0aa75wUUyTSaWR5DDYGoaSB6GTHCSQfEN_TVJ2dfFYQUdqYT2bNawhOQQ/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/15pJ1UsZbQYPsD9UKoxsJ6BMNu1145BiZbg8RAaioDRBpXE3cejiePttrXRSjZSR8UELacNgNlzwzmyk-D8e-gAlvGGG5qmDUzeoQuJJ0nEGm3haHcfwsJA2adigAEXUq0Ttt_hdyhKfCdhCNJXT63odzZE5kq8rnXOxo6eU099bh8I_kE0Zvgg68FKbtx2ynhwNEES68olxr3SUdeM_0rkv65vUq-jdp3K79nC2rmT7KMPxmpUbI3oyUOiZn23xmooFn1WhY3QB43D93dxYXBQ/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/1i3SXXd_VUaILJpE54pR41qAvJuGS21D1bDKw6bLMeXoZZoQQavFv60FJkyTayVIkW3k5RPNl3l_h94u9c4fzmk2Xe4WYLYhZ6hp0ZsRD2vuA1WioHOLtvC4RMKhP1RS0uFFe84qVbqoQX5MtBTXN0t2Ck5T2LuUSYqPeoDWHPfDl8AAs1-gpU0aDG5zhGnxhRNkyClTmAp4L9a8mNxy2oCGDPlZTuvV0Ykv1NUSwyBBQCZGmqJjcITDeTJAPbApjYYTRgy63qCtKxXrF5eEcFQ/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/15pJ1UsZbQYPsD9UKoxsJ6BMNu1145BiZbg8RAaioDRBpXE3cejiePttrXRSjZSR8UELacNgNlzwzmyk-D8e-gAlvGGG5qmDUzeoQuJJ0nEGm3haHcfwsJA2adigAEXUq0Ttt_hdyhKfCdhCNJXT63odzZE5kq8rnXOxo6eU099bh8I_kE0Zvgg68FKbtx2ynhwNEES68olxr3SUdeM_0rkv65vUq-jdp3K79nC2rmT7KMPxmpUbI3oyUOiZn23xmooFn1WhY3QB43D93dxYXBQ/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/1bSmbxcdto4UX-KyHltjOvd5ZOXIVw-EHeU4EZ-P-WLpYWWrECEjnSzc2KYuhlVuQkzp56Cfz5_17KP2_5JP3QCROMtPSKH47gxyefM_FigcxQHXOeOcivBKqo74lDNXjVJZjVxrFUoL_ybNRXnKSEbBpj9qeiIe9gZ5r-minn8jOtdG5553FZQOFWoIKHqtjQeuYULNhkqp7yPEpfgNqF0wFPzSzAww-8uQp3PGpNBe60u5KmuWUy85NYxhd4Ta3-pua4rf-5a1VucFhHWdC5A/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/1i3SXXd_VUaILJpE54pR41qAvJuGS21D1bDKw6bLMeXoZZoQQavFv60FJkyTayVIkW3k5RPNl3l_h94u9c4fzmk2Xe4WYLYhZ6hp0ZsRD2vuA1WioHOLtvC4RMKhP1RS0uFFe84qVbqoQX5MtBTXN0t2Ck5T2LuUSYqPeoDWHPfDl8AAs1-gpU0aDG5zhGnxhRNkyClTmAp4L9a8mNxy2oCGDPlZTuvV0Ykv1NUSwyBBQCZGmqJjcITDeTJAPbApjYYTRgy63qCtKxXrF5eEcFQ/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/11kLega6aHANPuoB9nMBwLhMhSyMrekdgO1JGgNJnsRUb4j_L79yVzmlZlrYHbRifj9A1gpecgEss9vc-tsg0JLzEoZBQklMnXiB-f5NZehZByUaBLzHRtPekB6Nf6H0HYCK6RqBQPVIqbzVY20w8i906jiCKWlMlbgdByBL9MP6HC6koL45cmF2XRJnBkbD7gDHVzr3J0Wljf4tqYwuiLgay_O3Em0aa75wUUyTSaWR5DDYGoaSB6GTHCSQfEN_TVJ2dfFYQUdqYT2bNawhOQQ/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/1i3SXXd_VUaILJpE54pR41qAvJuGS21D1bDKw6bLMeXoZZoQQavFv60FJkyTayVIkW3k5RPNl3l_h94u9c4fzmk2Xe4WYLYhZ6hp0ZsRD2vuA1WioHOLtvC4RMKhP1RS0uFFe84qVbqoQX5MtBTXN0t2Ck5T2LuUSYqPeoDWHPfDl8AAs1-gpU0aDG5zhGnxhRNkyClTmAp4L9a8mNxy2oCGDPlZTuvV0Ykv1NUSwyBBQCZGmqJjcITDeTJAPbApjYYTRgy63qCtKxXrF5eEcFQ/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/11kLega6aHANPuoB9nMBwLhMhSyMrekdgO1JGgNJnsRUb4j_L79yVzmlZlrYHbRifj9A1gpecgEss9vc-tsg0JLzEoZBQklMnXiB-f5NZehZByUaBLzHRtPekB6Nf6H0HYCK6RqBQPVIqbzVY20w8i906jiCKWlMlbgdByBL9MP6HC6koL45cmF2XRJnBkbD7gDHVzr3J0Wljf4tqYwuiLgay_O3Em0aa75wUUyTSaWR5DDYGoaSB6GTHCSQfEN_TVJ2dfFYQUdqYT2bNawhOQQ/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/1i3SXXd_VUaILJpE54pR41qAvJuGS21D1bDKw6bLMeXoZZoQQavFv60FJkyTayVIkW3k5RPNl3l_h94u9c4fzmk2Xe4WYLYhZ6hp0ZsRD2vuA1WioHOLtvC4RMKhP1RS0uFFe84qVbqoQX5MtBTXN0t2Ck5T2LuUSYqPeoDWHPfDl8AAs1-gpU0aDG5zhGnxhRNkyClTmAp4L9a8mNxy2oCGDPlZTuvV0Ykv1NUSwyBBQCZGmqJjcITDeTJAPbApjYYTRgy63qCtKxXrF5eEcFQ/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/1i3SXXd_VUaILJpE54pR41qAvJuGS21D1bDKw6bLMeXoZZoQQavFv60FJkyTayVIkW3k5RPNl3l_h94u9c4fzmk2Xe4WYLYhZ6hp0ZsRD2vuA1WioHOLtvC4RMKhP1RS0uFFe84qVbqoQX5MtBTXN0t2Ck5T2LuUSYqPeoDWHPfDl8AAs1-gpU0aDG5zhGnxhRNkyClTmAp4L9a8mNxy2oCGDPlZTuvV0Ykv1NUSwyBBQCZGmqJjcITDeTJAPbApjYYTRgy63qCtKxXrF5eEcFQ/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/11kLega6aHANPuoB9nMBwLhMhSyMrekdgO1JGgNJnsRUb4j_L79yVzmlZlrYHbRifj9A1gpecgEss9vc-tsg0JLzEoZBQklMnXiB-f5NZehZByUaBLzHRtPekB6Nf6H0HYCK6RqBQPVIqbzVY20w8i906jiCKWlMlbgdByBL9MP6HC6koL45cmF2XRJnBkbD7gDHVzr3J0Wljf4tqYwuiLgay_O3Em0aa75wUUyTSaWR5DDYGoaSB6GTHCSQfEN_TVJ2dfFYQUdqYT2bNawhOQQ/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
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>>>>
>>>> <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
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>>>> http://secure-web.cisco.com/11kLega6aHANPuoB9nMBwLhMhSyMrekdgO1JGgNJnsRUb4j_L79yVzmlZlrYHbRifj9A1gpecgEss9vc-tsg0JLzEoZBQklMnXiB-f5NZehZByUaBLzHRtPekB6Nf6H0HYCK6RqBQPVIqbzVY20w8i906jiCKWlMlbgdByBL9MP6HC6koL45cmF2XRJnBkbD7gDHVzr3J0Wljf4tqYwuiLgay_O3Em0aa75wUUyTSaWR5DDYGoaSB6GTHCSQfEN_TVJ2dfFYQUdqYT2bNawhOQQ/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
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>>>> <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
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>>>
>>> <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJqmPVauMgye27XenRCyW2RS0NRxLkcR1OoNBeHGUfzDoIp4j6b42zzPwQevNYKvmMb9nOxzG7B4sqbSRmGPPSkC-PWiTeMTc30aZjdjf857XnvJFeZuxSKRNefHfNFyZcQmwZqPAhPL5d1nOXJYwO429ya5ccWZe3Gbe_y0oLS5xGqhzJAXI7qCHxRjnCxI3nRz7nIkN3dQIDfurSNEi1EK1rmdSSlLc99qzHa8kP0w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>>
>>>
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>>> <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJqmPVauMgye27XenRCyW2RS0NRxLkcR1OoNBeHGUfzDoIp4j6b42zzPwQevNYKvmMb9nOxzG7B4sqbSRmGPPSkC-PWiTeMTc30aZjdjf857XnvJFeZuxSKRNefHfNFyZcQmwZqPAhPL5d1nOXJYwO429ya5ccWZe3Gbe_y0oLS5xGqhzJAXI7qCHxRjnCxI3nRz7nIkN3dQIDfurSNEi1EK1rmdSSlLc99qzHa8kP0w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
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