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 <gr...@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.dub...@gmail.com <mailto:jonathan.m.dub...@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 <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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: > > <5609ba16.2090...@nmr.mgh.harvard.edu > > <mailto:5609ba16.2090...@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 <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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: > > > <55ef2a23.3070...@nmr.mgh.harvard.edu > > <mailto:55ef2a23.3070...@nmr.mgh.harvard.edu>> > > <mailto:55ef2a23.3070...@nmr.mgh.harvard.edu > > <mailto:55ef2a23.3070...@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>> > > <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 > > gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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.html > >Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > 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 > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > 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 > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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