Reading values from overlays with PETcoreg - Freesurfer

8 Jan 2016

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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