-------- Forwarded Message -------- Subject: Re: [Freesurfer] PVE correction tool within the V 6 beta Date: Thu, 1 Oct 2015 17:08:07 +0200 (CEST) From: [email protected] To: Freesurfer support list <[email protected]> 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" <[email protected]> À: [email protected] 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
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