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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.ottoy@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.ottoy@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. <DGREVE@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. <DGREVE@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.ottoy@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

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

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

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

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

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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