External Email - Use Caution Thank your very much Douglas for the information. Much appreciated.
On Tue, Jan 28, 2020 at 1:12 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > The symmetric GTM is the default (the non-sym is not implemented). > > I highly recommend that you don't use melzter (which is why I did not have > docs for it:). But if you must run it, add --melzter BinThresh MaskThresh > nDilations > BinThresh is used to create a binary mask by thresholding the WM+GM tissue > fraction maps at BinThresh. This is a number between 0 and 1 > nDilations is the number of times that the binary mask is dilated to > expand it a bit (don't use more than 2) > MaskThresh - the binarized mask is smoothed and then divided into the PET > image to do the correction. Voxels whose smoothed value is less than > MaskThresh is set to 0. MaskThresh should be between 0 and 1 > > this is all kind of messy and unprincipled and the results are very > sensitive to the values you set above . which is why I avoid it. > > On 1/27/2020 9:23 PM, Kate Marvel wrote: > > External Email - Use Caution > Thanks Douglas. > > I checked the mri_gtmpvc --help command but the arguments for symmetric > Geometric Transfer Matrix and two-component model (Meltzer) > are missing. See the output below: > > USAGE: mri_gtmpvc > > --i inputvol : source data to PVC > --frame F : only process 0-based frame F from inputvol > --psf psfmm : scanner PSF FWHM in mm > --seg segfile : anatomical segmentation to define regions for GTM > --reg reg.lta : LTA registration file that maps anatomical to PET > --regheader : assume input and seg share scanner space > --o outdir : output directory > > --mask volfile : ignore areas outside of the mask (in input vol space) > --auto-mask FWHM thresh : automatically compute mask > --no-reduce-fov : do not reduce FoV to encompass automask > --C contrast.mtx : univariate contrast to test (ascii text file) > > --default-seg-merge : default schema for merging ROIs > --merge-hypos : merge left and right hypointensites into to ROI > --merge-cblum-wm-gyri : cerebellum WM gyri back into cerebellum WM > --tt-reduce : reduce segmentation to that of a tissue type > --replace Id1 Id2 : replace seg Id1 with seg Id2 > --replace-file : file with a list of Ids to replace > --reg-identity : assume that input is in anatomical space > --rescale Id1 <Id2...> : specify reference region(s) used to rescale > (default is pons) > --no-rescale : do not global rescale such that mean of reference > region is scaleref > --scale-refval refval : scale such that mean in reference region is > refval > > --no-tfe : do not correction for tissue fraction effect (with --psf 0 > turns off PVC entirely) > --rbv : perform RBV PVC > --rbv-res voxsize : set RBV voxel resolution (good for when standard > res takes too much memory) > --mg gmthresh RefId1 RefId2 ...: perform Mueller-Gaertner PVC, gmthresh > is min gm pvf bet 0 and 1 > --mg-ref-cerebral-wm : set MG RefIds to 2 and 41 > --mg-ref-lobes-wm : set MG RefIds to those for lobes when using wm > subseg > --mgx gmxthresh : GLM-based Mueller-Gaertner PVC, gmxthresh is min gm > pvf bet 0 and 1 > --km-ref RefId1 RefId2 ... : compute reference TAC for KM as mean of > given RefIds > --km-hb RefId1 RefId2 ... : compute HiBinding TAC for KM as mean of > given RefIds > --ss bpc scale dcf : steady-state analysis spec blood plasma > concentration, unit scale > and decay correction factor. You must also spec --km-ref. Turns off > rescaling > > --X : save X matrix in matlab4 format as X.mat (it will be big) > --y : save y matrix in matlab4 format as y.mat > --beta : save beta matrix in matlab4 format as beta.mat > --X0 : save X0 matrix in matlab4 format as X0.mat (it will be big) > --save-input : saves rescaled input as input.rescaled.nii.gz > --save-eres : saves residual error > --save-yhat : saves yhat > --save-yhat-with-noise seed nreps : saves yhat with noise, seed < 0 for > TOD > --save-yhat-full-fov : saves yhat in full FoV (if FoV was reduced) > --save-yhat0 : saves yhat prior to smoothing > > --synth gtmbeta C R S MBs seed nreps : synthesize volume with gtmbeta > as input > spec all other inputs the same; CRS are PSF for col, row, slice, > MBs motion blur slope > seed=0 for no noise, -1 for TOD seed. Turns on VFC for synth > but returns it to its specified value for analysis > --synth-only : exit after doing synthesis (implies --synth-save) > --synth-save : with --synth saves synthesized volume to > outdir/synth.nii.gz > > --threads N : use N threads (with Open MP) > --max-threads : use the maximum allowable number of threads for this > computer > --max-threads-minus-1 : use one less than the maximum allowable number > of threads for this computer > --sd SUBJECTS_DIR > --vg-thresh thrshold : threshold for 'ERROR: LTAconcat(): LTAs 0 and 1 > do not match' > --gdiag diagno : set diagnostic level > --debug turn on debugging > --checkopts don't run anything, just check options and exit > --help print out information on how to use this program > --version print out version and exit > > Thanks, > > On Mon, Jan 27, 2020 at 6:03 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Run it with --help. Also look at the PETsurfer wiki page for typical usage >> >> On 1/27/2020 3:54 PM, Kate Marvel wrote: >> >> External Email - Use Caution >> Hi Freesurfer community, >> >> I would like to know the arguments to use for symmetric Geometric >> Transfer Matrix and two-compartment model (Meltzer Method) in the >> petsurfer command "mri_gtmpvc". >> >> Thank you, >> >> -- >> kate >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > kate > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate
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