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