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> 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> >> Subject: Re: [Freesurfer] PET tools in FS dev v6.0 >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <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 >> > sysname Darwin >> > hostname Jons-MacBook-Air.local >> > machine x86_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>> >> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0 >> > To: 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>> >> > 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>> >> > https://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 >> -- >> 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 > > > 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. > >
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