Re: [Freesurfer] Failed tissue type check {Disarmed}

Douglas N. Greve Thu, 15 Apr 2021 09:10:48 -0700

Hi Julie, sorry for the delay. The issue here is in finding the rightsegmentation for the replacement. Try --replace 29 24. TheLeft-undetermined voxels are actually in ventricle, so 24 replaces themwith CSF. I ran it on your data, and it finished without error.


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 withthe non-pvc data.


Thanks
Julie

On Tue, 2 Feb 2021 at 11:10, Julie Ottoy <julie.jj.ot...@gmail.com<mailto: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 <mailto: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 <mailto:dgr...@mgh.harvard.edu>> wrote:

            Try using --replace 29 2


            On 12/29/2020 12:48 PM, Julie Ottoy wrote:


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            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 <mailto: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:


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                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
                <mailto:julie.jj.ot...@gmail.com>> wrote:

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                          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
                          
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                    Douglas Greve
                    
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                        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

                        --
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                        Principal Scientist, Biomarker Experimental Medicine 
Leader
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                          Re: [Freesurfer] mri_gtmpvc error: failed
                          tissue type check
                          
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                    2016-11-09
                    
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                    Douglas N Greve
                    
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                        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

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                        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.

                        >
                        >
                        >
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                          Re: [Freesurfer] mri_gtmpvc error: failed
                          tissue type check
                          
<https://secure-web.cisco.com/1yv39xApOHJ3FS6xDcFycnMnbHtStZeNBiLl3QzfL8G4yuWqEeGFNYzyiQ33Ex-jCBtvZpJntii832vSyEk6xnN5IYHn5Srf9NA5CmqjyBtwhPnmxD_EsoeCGDEQW0hG5N_lDc1_iosQAG4k2qZ26umeGpKNIFRfSyM1nISnBVv4YTEoBjMQuweEKSCvNNFAmb-kDbh7mk-1AukTjK5yO0vqnjqi1AaUaaKOobt0r0FKGBTu7BfRTZB69YmwQv6W9R_6kXsldmgOPEtybOxAaig/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50024.html>

                    2016-11-09
                    
<https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkAZk8D_towDhzokqKY_qAQwhvC1t3LAMD69EKL6P5LScJWmhzwCjRBuSg7VzqL6g83C8d5pyJjtz5eqtsIlEQN85STIBFvGtUVLKU2XG0l5kr78h30dIzDum_UKXAyP_jpbOnx_VKSbmtieMeOYTumJYcyCcdTfrnLSUO4WN-kp10g8XORxRwDJZA_c02mHkmmEuJCXGaPsflUoQJRc3evAQquLrXiu8gGFbfE5ayEQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Ddate%3A20161109%26o%3Dnewest%26f%3D1>
                    Thread
                    
<https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwaUaNLzzolPe0sGFdV5PJBoevMcJ1RAbNloWllE1g0lj1EW8LD2TZbjEOIdDEMriGji9_hbC3Px8BfDnBzOlNFrAOvbnbGfZrX3w9x2LGcKlY2lE-Dl-8pOACnRlmoVrY07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2Bcheck%2522%26o%3Dnewest%26f%3D1>
                    Donatas Sederevicius
                    
<https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKlwU3UP25xnszjeeOUSTu4MAOtS07GmVt_x7VvtqpQoEAaS71PvpUOuuh2Jakccv8UApdQNTlnQdUnmjNnHmlGvLcg5IUijE2zaZXa9RYA8IDK_ah32UsYDVwGsJEoTOmWJw7z4syagjpNSb-3Md12zplk8Bk_VyLPOioLaFuLwkId-HkmUwYihnJP3FHPaoBvcC9nZcNp9aLf_oWZSt-7iToV4Zqf-IpHtddQTUy0A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Donatas%2BSederevicius%2522%26o%3Dnewest%26f%3D1>

                        I followed the processing workflow as described in 
PETSurfer wiki and
                        gtmseg.mgz was created using gtmseg script as 
described. I ran this processing
                        for over 100 subjects and only one has failed.
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                          Re: [Freesurfer] mri_gtmpvc error: failed
                          tissue type check
                          
<https://secure-web.cisco.com/1vPxlf-9EcToYjQ2NcohNFPvheryGJhjZq4nxdkmbOKRg2omA5NkvMb0IblIRORZ1EoUy_uNZK78n0cJGkdzgNLgkKgbgrH6CwMUbGRrwurpX7PEF7YXvBsk3iQvBzt9B4WWXE2dF2qCPythWj_9RDNWO3rOCKW7J8-CFgKSLi4xVEHJtYnueAy-zQquTDSQGbXCyL47s3SpPzQZ6RX88M2Qf0zVigwKGWTeW9-6AOasIs7vnUUsbSasf1jSg1sKh9CeEzsLQstjOfhvzBEhNEg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50018.html>

                    2016-11-09
                    
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                    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



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                          [Freesurfer] mri_gtmpvc error: failed
                          tissue type check
                          
<https://secure-web.cisco.com/1-KTvEDdAuFhtSF_p9XP0T2HYXV7p_VXGloR253IuV-slWQ30G_xnBl6OTD1xVEPHwQNraHUfoMiBn--OpbsCNvDeeg2yiiTFt_hNb9tG0rZs036N4J30PcPcxMbEeZJd8UKhBiWZIXXd3HJmU4EZDdWNusOUttj4KzgwnxJ_kQQSNjfFaZ3_2BQfSq-0GcHekQ-tjX1TcaUz5rYKp9tVt4pQNGbVmyUka548gRcJpGDFOGvz-1U_S6hDUcWvOKfrllmBmNeaQVTIHWSXmZZkhA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg50013.html>

                    2016-11-09
                    
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                    Thread
                    
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                    Donatas Sederevicius
                    
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                        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
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Re: [Freesurfer] Failed tissue type check {Disarmed}

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