I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz outputs looked fine:
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
mri_gtmseg --s $s
etc, exited fine

Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error:
[weckl:FDG_2017-11-15] (nmr-stable6-env) cat MR_2017-11-07/pvc.psf06/mri_gtmpvc.log
$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 --rbv --mgx .25 --lgtm --threads 8 --seg gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg $PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge
sysname  Linux
hostname weckl.nmr.mgh.harvard.edu
machine  x86_64
user     makaretz
vgthresh   0.001000
nReplace   18
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz
Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab
Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta
Failed tissue type check
[weckl:FDG_2017-11-15] (nmr-stable6-env)

I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this thread (I left out --no-xcerseg since I think it's now the default): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.html But I got a different error, where it's trying to write to a file called (null):
[weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
cwd $PET_DIR
cmdline mri_gtmseg --s $s--keep-cc
sysname  Linux
hostname weckl.nmr.mgh.harvard.edu
machine  x86_64
user     makaretz
subject $s
USF 2
OutputUSF 2
apasfile apas+head.mgz
wmannotfile NULL
ctxannotfile aparc.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   1
dmax 5.000000
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz
Loading surfaces  t = 2.1280
Loading annotations  t = 6.2390
Not segmenting WM
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
     nthreads = 1
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
     nthreads = 1
Upsampling segmentation USF = 2 t = 32.3010
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using aparc.annot t = 83.9890
  MRIannot2CorticalSeg(): looping over volume
     nthreads = 1
  MRIannot2CorticalSeg(): found 1517 unknown, filled with 257
Not subsegmenting WM
Found 115 segs in the final list
MRIgtmSeg() done, t = 358.8340
Computing colortable
WARNING: segid   29 Left-undetermined tissue type is not set
Writing output file to $SUBJECTS_DIR/$s/mri/(null)
unknown file type for file ($SUBJECTS_DIR/$s/mri/(null))
[weckl:FDG_2017-11-15] (nmr-stable6-env)

I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). Do you have any advice?

Thank you in advance for any help!
Sara