I think I see the problem. When you run gtmseg, you need to add
--keep-cc. You can rerun it using the previous command line, but add
--keep-cc and --no-xcerseg. The second option tells it not to redo the
extracerebral segmentation (which won't change with CC)

On 01/29/2016 11:21 AM, Pradeep wrote:
> Thank you for the response.
>
> Here is my full command log with error
>
>
> $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
>
> $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> gtmpvccc.output
> Loading input t12pet.nii.gz
>   done loading input 1 frames
>
> $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> cd /analysis/software_test/fs6pvc/******/mri
> mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> gtmpvccc.output
> sysname  Linux
> hostname server
> machine  x86_64
> user     user
> vgthresh   0.001000
> nReplace   18
> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 9 avail.processors, using 9
> Creating output directory gtmpvccc.output
> Loading seg for gtm gtmseg.mgz
> Loading seg ctab gtmseg.ctab
> Reading gtmseg.lta
> Replacing 18
> ERROR: CheckSegTissueType() no entry for seg 192
> Failed tissue type check
>
>
> Thanks,
> Pradeep
>
>
> On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>
>     On 01/28/2016 06:50 PM, Pradeep wrote:
>     > Hello Doug,
>     >
>     > I have used the gtmseg with --keep-cc  flag and the
>     corresponding ctab
>     > files showed the labels but the mri_gtmpvc step failed.
>     > ****
>     > Loading seg for gtm gtmseg.mgz
>     > Loading seg ctab gtmseg.ctab
>     > Reading gtmseg.lta
>     > Replacing 18
>     > ERROR: CheckSegTissueType() no entry for seg 192
>     > Failed tissue type check
>     > ****
>     What is your mri_gtmpvc command line? What is the rest of the terminal
>     output?
>     > My objective is to use the combination of all CC's as a reference
>     > region and obtain the PVC results, which would be listed in
>     gtm.stats.dat
>     It will be best to combine them when running mri_gtmpvc using
>     --replace,
>     eg, --replace 252 251 --replace 253 251 --replace 254 251
>     --replace 255 251
>     this will cause all segments of the CC to appear to be a single
>     segment
>     (251).
>     >
>     > Also, I read in the previous email discussions that the default
>     > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with
>     > another ROI as a reference region,
>     > would it be OK take a ratio of the ROI's in gtm.stats.dat table.
>     Yes, or you can spec the new region, eg --rescale 251
>     >
>     > Thanks,
>     > Pradeep
>     >
>     > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve
>     > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

>     <mailto:greve@nmr.mgh.harvard.edu

>     <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>     >
>     >
>     >     If you want to use partial volume correction, then you are
>     better off
>     >     using mri_gtmpvc with the bbr registration, something like
>     >
>     >     1. To start, run
>     >
>     >     gtmseg --s subject
>     >
>     >     This will take a couple of hours and produces some files needed
>     >     for GTM
>     >     PVC (which is used for GTM, MG, RBV).
>     >
>     >     2. You'd then register the PET to the anatomical with bbregister
>     >     (probably with --t2 weighting). Make sure to save the output
>     as an LTA
>     >     (--lta). I usually use the mean TAC as the input. You can do
>     this in
>     >     parallel with #1.
>     >
>     >     3. You'd then run mri_gtmpvc, something like
>     >
>     >     mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg
>     >     gtmseg.mgz
>     >     --reg reg.lta --default-seg-merge  --o gtmpvc.output
>     >
>     >     PSF is the point-spread FWHM of the scanner; reg.lta is the
>     >     registration from #2. By default, this will scale by pons.
>     The output
>     >     will be gtm.stats.dat and gtm.nii.gz. They both basically
>     have the
>     >     same information. gtm.stats.dat is an easy to read text
>     file. Where
>     >     each row is an ROI, something like:
>     >
>     >     9   17 Left-Hippocampus subcort_gm       473
>     >     174.083        1.406       0.1216
>     >
>     >     9 = nineth row
>     >     17 = index for RO
>     >     Left-Hippocampus = name of ROI
>     >     subcort_gm = tissue class
>     >     473 = number of PET voxels in the ROI
>     >     174 = variance reduction factor for ROI (based on GLM/SGTM)
>     >     1.406 = PVC uptake of ROI relative to Pons
>     >     0.1216 = resdiual varaince across voxels in the ROI
>     >
>     >     gtm.nii.gz is a nifti file with each "voxel" being an ROI.
>     The value
>     >     is the PVC uptake of ROI relative to Pons. These can easily be
>     >     concatenated together (mri_concat) and used as input to
>     mri_glmfit
>     >     for group analysis.
>     >
>     >
>     >
>     >
>     >     On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
>     >     > Dear Freesurfer experts!
>     >     >
>     >     > I am currently working on PET analysis using FS
>     >     >
>     >     > I coregistered my PET with the processed MR using bbregister,
>     >     > transfered it to a surface using mri_vol2surf
>     >     > and now createt an overlay in freeview with the
>     lh.inflated and
>     >     used the
>     >     > labels from the lh.aparc.a2009s.annot file.
>     >     >
>     >     > In freeview i get the corresponding BP value for each
>     vertex now but
>     >     > is there a way to get a list of vertices with the
>     corresponding
>     >     BP value
>     >     > and the corresponding ROI this vertex belongs to?
>     >     > Or is there a better to do this analyis?
>     >     >
>     >     > Many thanks in advance!
>     >     >
>     >     > Benjamin
>     >     >
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
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MGH-NMR Center
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