-------- Forwarded Message --------
Dear Greve,
Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some unclear options (e.g. --mgx .01)
Could you please explain which method is used for the pve correction and how can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of all regions?
Many thanks for your help,
Best,
Mohamed
----- Mail original -----
De: "Douglas Greve" <greve@nmr.mgh.harvard.edu>
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Lundi 28 Septembre 2015 17:49:49
Objet: Re: [Freesurfer] PVE correction tool within the V 6 beta
I'm still putting all the documentation together, but you can start with the instructions below. They are assuming you will use kinetic modeling. If you have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 not needed. Let me know and I can give you further instructions.
doug
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 (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 tac.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. --km-hb specifies the highbinding region for MRTM2. --km-ref specifies the reference region. --mgx specifies to output a muller-gartner map (not necessary for GTM ROI analysis).
4. For the GTM (ROI) MRTM1 KM analysis, you would then run
mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz
where time.dat is a text file withe acquisition time of each time point in the tac.
5. For the MRTM2 analysis
set k2p = `cat mrtm1/k2prime.dat`
mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o mrtm1 --no-est-fwhm --nii.gz
If you want to run a voxel-wise analysis, then you can use the mgx
volume as input (--y). Probably you'll want to sample this to the
surface using mri_vol2surf and the registration file aux/anat2pet.lta,
then smooth on the surface
On 9/28/15 11:38 AM, Mohamed Ali Bahri wrote:
> Dear Expert,
>
> Are there any explanation (steps to follow) about the use of FreeSurfer
> (version 6 beta) to correct for the partial volume effect (PET dynamic
> data)?
>
> Many thanks in advance,
>
> Best,
>
> Mohamed
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.