Re: [Freesurfer] Reading values from overlays with PETcoreg

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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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