Hi Mohamed, sorry, I have not fully documented the procedure yet. I've put some notes below 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 10/27/2015 04:47 PM, Mohamed Ali Bahri wrote: > Dear Bruce, > > Am I missed the answer of Dr. Greve about the following questions? > > Is it possible to tell what are the implemented methods for the PET pve > correction? and how we can > obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)? > > > Many thanks, > > Mohamed > > > > On 26/10/15 14:52, Bruce Fischl wrote: >> oh, then I'll leave it for Doug >> Bruce >> On Mon, 26 Oct 2015, Mohamed Ali Bahri >> wrote: >> >>> Hi Bruce, >>> >>> Yes, for PET analysis. >>> >>> Best, >>> >>> Mohamed >>> >>> On 26/10/15 14:45, Bruce Fischl wrote: >>>> Hi Mohamed >>>> >>>> do you mean for PET analysis or for the recent paper that Rebecca Shafee >>>> wrote on e.g. tissue intensity properties? >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> >>>> On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote: >>>> >>>>> Is it possible to tell what are the implemented methods? and how we can >>>>> obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)? >>>>> >>>>> Best, >>>>> >>>>> Mohamed >>>>> >>>>> On 26/10/15 13:27, Bruce Fischl wrote: >>>>>> no, sorry, we haven't had time to document it >>>>>> On Mon, 26 Oct 2015, >>>>>> [email protected] wrote: >>>>>> >>>>>>> Dear FreeSurfer Experts, >>>>>>> >>>>>>> Are there any documentation comes out for the pve correction tool >>>>>>> implemented in the FreeSurfer V6? >>>>>>> >>>>>>> Many thanks in advance, >>>>>>> >>>>>>> Best, >>>>>>> >>>>>>> Mohamed >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> [email protected] >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> [email protected] >>>>>> 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. >>>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
