Re: [Freesurfer] Reading values from overlays with PETcoreg

The problem is that --default-seg-merge merges the CC with WM, so you can't use that option, which means that you'll have to specify the rest of the default seg merge manually. You can do this with more --replace args or you can create a file. If you've been able to run mri_gtmpvc without the current replace, then it will create a replacement file in the aux folder. Get that, remove the 251 entry, and change the 252-255 entries to point to 251

On 01/29/2016 02:12 PM, Pradeep wrote:

Unfortunately, that did not fix the problem.

Here is what I did 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors

3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output Loading input t12pet.nii.gz done loading input 1 frames ERROR: item 251 appears as both source and target seg id in replacement list

$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/128_S_0225_v06/mri mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output sysname Linux hostname machine x86_64 user vgthresh 0.001000 nReplace 22 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 9 avail.processors, using 9 Creating output directory gtmpvcrcc.output Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 22 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check

Thank you for looking into this, Pradeep

On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
<mailto: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>>
>     <mailto: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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