Re: [Freesurfer] PET tools in FS dev v6.0

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
    >     >
    >     >
    >     > _______________________________________________
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    >     >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>
    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing:
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