On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve <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>> 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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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
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> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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