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
>
> _______________________________________________
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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--
kate
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