oops, sorry for the delay. You are probably right that it has to do with the big vents. There must be some obscure label that gets created for which the tissue type is unknown to the gtm. But there should have been more info in the terminal output. Can you send me everything it prints out?

On 7/1/2019 7:49 PM, Lois Gomez, Cristina wrote:
Hi Doug,

Thanks for you quick response.  Here is some info about the command line and output.
-----------------------
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR $SUBJECTS_DIR
mri_gtmpvc --auto-mask 11 .001 --mgx .25 --lgtm --threads 8 --seg gtmseg.mgz --no-rescale --save-input --i $PET_DIR/cr_early_MeanCPS.nii --reg  $PET_DIR/reg.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge 
sysname  Linux
hostname rincewind.nmr.mgh.harvard.edu
machine  x86_64
user     clois
vgthresh   0.001000
nReplace   18
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Loading seg for gtm $SUBJECTS_DIR/mri/gtmseg.mgz
Loading ctab $SUBJECTS_DIR/gtmseg.ctab
Reading $SUBJECTS_DIR/mri/gtmseg.lta
Failed tissue type check
--------------------

I am including a couple of screenshots, as the error seems to be related to the subject's anatomy. After running the initial recon-all, there was a big whole in the wm.mgz (and the surfaces were wrong and excluded a big portion of the brain), so we filled it with wm voxels. The surfaces look now fine and there is no whole in the wm.mgz , but that has not solved the 'Failed tissue type' problem. Is there a more appropriate way to edit this case, so that we are able to run the pvc?  

Let me know if this helps or you need any additional information. 

Many thanks in advance,
Cristina
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Monday, July 1, 2019 6:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_gtmpvc -- Failed tissue type check
 
Hi Cristina, can you send more info? Eg, your command line and terminal output. Do you do anything special (eg, your own annotation)?

On 7/1/2019 5:57 PM, Lois Gomez, Cristina wrote:
Hi Freesurfers,

I am having trouble with one subject's PVC (we process many cases and never had this issue before). 
When running mri_gtmpvc I get a 'Failed tissue type check' error. 

I've seen that other people have reported similar errors in the past, but I haven't found any advice on how to trouble-shoot this. 
We have longitudinal PET data with two tracers for this subject, so it is very important for us to get this fixed. Any advice?  

Thank you,
Cristina

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