External Email - Use Caution
Dear FreeSurfer experts,
I am a student in neuroimaging using FreeSurfer. I have some questions and I don't know where to send questions. That's why I found this mail and writing.
I've studied PetSurfer for partial volume correction of PET. I saw the tutorial in website. Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.
After generating gtmseg and coregistration to make lta file, I followed this code and changed some.
*mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz * *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv --o output_pvc*
After this, rbv.nii.gz file was generated. and SUVR analysis was performed as reference region (cerebellar cortex). But Compared to original un-pvc PET, Cortex SUVR was reduced...
In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.
Is is okay if I use the output file as rbv.nii.gz ?
in Thomas et al, 2011, He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions. Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET using RBV method)
In that case, What are the regions to make rbv.nii.gz method in PetSurfer?
Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?
If not, Please tell me what is the correct command of mri_gtmpvc. I need only partial volume corrected PET using RBV method.
Sincerely,
Soo-Jong Kim
On 11/15/19 4:19 AM, Soo-Jong Kim wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am a student in neuroimaging using FreeSurfer. I have some questions and I don't know where to send questions. That's why I found this mail and writing.
I've studied PetSurfer for partial volume correction of PET. I saw the tutorial in website. Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.
After generating gtmseg and coregistration to make lta file, I followed this code and changed some.
*mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz * *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv --o output_pvc*
After this, rbv.nii.gz file was generated. and SUVR analysis was performed as reference region (cerebellar cortex). But Compared to original un-pvc PET, Cortex SUVR was reduced...
In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.
Is is okay if I use the output file as rbv.nii.gz ?
Yes, it does work. Is your tracer one where you expect GM > WM?
in Thomas et al, 2011, He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions. Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET using RBV method)
In that case, What are the regions to make rbv.nii.gz method in PetSurfer?
Look in aux/seg.ctab (you can visualize the aux/seg.nii.gz)
Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?
Yes
If not, Please tell me what is the correct command of mri_gtmpvc. I need only partial volume corrected PET using RBV method.
Sincerely,
Soo-Jong Kim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Soo-Jong Kim