On Wed, Nov 18, 2015 at 10:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

For single frame, you can just run
mri_convert input.nii output.nii --frame F
where F is the 0-based frame number, then run mri_gtmpvc on output.nii

The PVC "image" is a bit tricky. You can get a muller-gartner image
(--mgx) or region-based voxel-wise (RBV) image with --rbv.

On 11/18/2015 12:36 PM, Pradeep wrote:
> Hello Doug,
>
> I am in the process of testing the FS PVC procedure and I was
> wondering if there is a way to do this procedure with single frame PET
> data and get the partial volume corrected SUVR image. I know that this
> is still new and not all the processes is documented yet, but any
> inputs on this would be appreciated. I have successfully ran steps 1
> and 2 from the process you have outlines above.
>
> Thanks,
> Pradeep
>
> On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois
> <jonathan.m.dubois@gmail.com <mailto:jonathan.m.dubois@gmail.com>> wrote:
>
> Hi Doug,
>
> I uploaded the files you requested. I'm not sure if it matters,
> but one thing I forgot to mention was that in order to get the pet
> file in the right format and orientation, I ended up using
> (ecattominc pet.v pet.mnc) and (itk_convert --inv-y --inv-x
> pet.mnc pet.nii). I couldn't find a good tool to convert directly
> form ECAT to NIFTI, but perhaps this conversion process interferes
> with the pet processing?
>
> Best,
> Jonathan
>
> Message: 7
> Date: Mon, 28 Sep 2015 18:07:18 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>Message-ID:
> <5609BA16.2090006@nmr.mgh.harvard.edu
> <mailto:5609BA16.2090006@nmr.mgh.harvard.edu>>

> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Can you upload the FS subject, pet data, and .lta?
> https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
>
> On 09/28/2015 12:08 PM, Jonathan DuBois wrote:
> > Hi Doug,
> >
> > I was told you were away last week so I'm reposting this message.
> > Thanks for sending me the information on the PET scripts. I
> > ran gtmseg, and bbregister successfully (I inspected both and they
> > look accurate), but I am getting a segfault with mri_gtmpvc at the
> > auto mask step.
> >
> > I copied the command and the error below. I thought that it could be a
> > memory issue due to the size of the matrix (I ran it on a mac with
> > 8gb) but I also tried to run it with the --tt-reduce and got the same
> > error. The data is from an HRRT PET scanner with a PSF of 4mm. For the
> > auto-mask input I used 6 .01, as your instructions were PSF+2. Is this
> > correct?
> >
> > Thanks
> > Jonathan
> >
> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.mgz --reg
> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > Loading input pet.nii.gz
> > done loading input 26 frames
> >
> > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $
> > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub
> > cd /Volumes/my_passport/external/Documents/fssub2/test
> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.mgz --reg
> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > sysnameDarwin
> > hostname Jons-MacBook-Air.local
> > machinex86_64
> > user jonathandubois
> > vgthresh 0.001000
> > nReplace 18
> > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> > 4 avail.processors, using 1
> > Creating output directory gtmpvc.output
> > Loading seg for gtm
> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.mgz
> > Loading seg ctab
> > /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.ctab
> > Reading /Users/jonathandubois/data/fssub/epc_111102/mri/gtmseg.lta
> > Replacing 18
> > Pruning ctab
> > done with seg vol
> > maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
> > Computing auto mask
> > Segmentation fault: 11
> >
> >
> > Message: 13
> > Date: Tue, 08 Sep 2015 14:34:11 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>

> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> > To:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>Message-ID:
> > <55EF2A23.3070705@nmr.mgh.harvard.edu
> <mailto:55EF2A23.3070705@nmr.mgh.harvard.edu>>
> <mailto:55EF2A23.3070705@nmr.mgh.harvard.edu

> <mailto:55EF2A23.3070705@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> > Yes there are both. For KM we have MRTM1 and MRTM2 so far. They
> > are not
> > well documented yet.
> > 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.
> >
> >
> > doug
> >
> >
> >
> > On 09/08/2015 02:11 PM, Jonathan DuBois wrote:
> > > Hi FS experts,
> > >
> > > In FS development package I see that there have been tools added for
> > > partial volume correction of PET data, but I was wondering if
> there
> > > were also kinetic modeling tools similar to those described in
> > Doug's
> > > 2014 paper? If you could let me know what PET processing
> tools have
> > > been included in the dev package, I would be interested to
> test and
> > > compare them.
> > >
> > > Thanks,
> > > Jonathan
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > >Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>

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> >
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358
> <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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