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
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