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.
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 > > > > > > _______________________________________________ > > 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 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 <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
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 <greve@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.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 thismessage.
> Thanks for sending me the information on the PET scripts. I > ran gtmseg, and bbregister successfully (I inspected both andthey
> look accurate), but I am getting a segfault with mri_gtmpvc atthe
> auto mask step. > > I copied the command and the error below. I thought that itcould be a
> memory issue due to the size of the matrix (I ran it on a macwith
> 8gb) but I also tried to run it with the --tt-reduce and gotthe 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 filesneeded
> for GTM > PVC (which is used for GTM, MG, RBV). > 2. You'd then register the PET to the anatomical withbbregister
(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 inparallel
> 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 forMRTM2. --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 ofeach 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 usethe mgx
> volume as input (--y). Probably you'll want to sample thisto 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 beentools added for
> > partial volume correction of PET data, but I waswondering if
there > > were also kinetic modeling tools similar to thosedescribed 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 interestedto
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 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 <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.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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yes, that is correct.
On 11/19/15 11:07 AM, Pradeep wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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.dubois@gmail.com <mailto:jonathan.m.dubois@gmail.com> <mailto: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> > <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: > <5609BA16.2090006@nmr.mgh.harvard.edu <mailto:5609BA16.2090006@nmr.mgh.harvard.edu> > <mailto: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>>> > <mailto: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:To%3Afreesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > <mailto: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>>> > <mailto: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 > > > > > > > > > _______________________________________________ > > > 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>>> > <mailto: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> > <mailto: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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto: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 <mailto: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 <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 <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
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Douglas Greve -
Douglas N Greve
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Pradeep