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 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 been tools addedfor
> partial volume correction of PET data, but I was wondering ifthere
> were also kinetic modeling tools similar to those described in Doug's > 2014 paper? If you could let me know what PET processing toolshave
> been included in the dev package, I would be interested to testand
> 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.