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:

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

2017-11-25 Thread Douglas Greve

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

2016-11-09 Thread Douglas N Greve

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

2016-11-09 Thread Donatas Sederevicius

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

2016-11-09 Thread Douglas Greve

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

2016-11-09 Thread Donatas Sederevicius

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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