Failed tissue type check {Disarmed} - Freesurfer

18 Dec 2020

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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
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
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 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
--
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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
https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r61...
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
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-- 
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MGH-NMR Centergr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
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2016-11-09
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 Donatas Sederevicius
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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
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2016-11-09
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 Douglas Greve
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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
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2016-11-09
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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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