Thank you for the response Doug!
The PET images I have are static images. Six * 5 min frames which I have summed together after realigning.
mri_gtmpvc --i summed.nii --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output
This command has worked and I just wanted to conform if it the correct way to use it.
-Pradeep
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 thismessage.
> Thanks for sending me the information on the PET scripts. I > ran gtmseg, and bbregister successfully (I inspected both andthey
> look accurate), but I am getting a segfault with mri_gtmpvc atthe
> auto mask step. > > I copied the command and the error below. I thought that itcould be a
> memory issue due to the size of the matrix (I ran it on a macwith
> 8gb) but I also tried to run it with the --tt-reduce and gotthe 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 filesneeded
> for GTM > PVC (which is used for GTM, MG, RBV). > 2. You'd then register the PET to the anatomical withbbregister
(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 inparallel
> 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 forMRTM2. --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 ofeach 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 usethe mgx
> volume as input (--y). Probably you'll want to sample thisto the
> surface using mri_vol2surf and the registration fileaux/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 beentools added for
> > partial volume correction of PET data, but I waswondering if
there > > were also kinetic modeling tools similar to thosedescribed 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 interestedto
test and > > compare them. > > > > Thanks, > > Jonathan > > > > > > _______________________________________________ > > Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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