Re: [Freesurfer] PET tools in FS dev v6.0
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 <gr...@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.dub...@gmail.com <mailto: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 > > <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: > > <5609ba16.2090...@nmr.mgh.harvard.edu > > <mailto: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_02/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_02/mri/gtmseg.mgz
Re: [Freesurfer] PET tools in FS dev v6.0
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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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.dub...@gmail.com <mailto:jonathan.m.dub...@gmail.com>
<mailto:jonathan.m.dub...@gmail.com
<mailto: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
<mailto:gr...@nmr.mgh.harvard.edu>
> <mailto: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>
> <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>Message-ID:
> <5609ba16.2090...@nmr.mgh.harvard.edu
<mailto:5609ba16.2090...@nmr.mgh.harvard.edu>
> <mailto:5609ba16.2090...@nmr.mgh.harvard.edu
<mailto: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_02/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 fra
Re: [Freesurfer] PET tools in FS dev v6.0
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_02/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_02/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. 0. 0. 0. 0. 0. >> > 4 avail.processors, using 1 >> > Creating output directory gtmpvc.output >> > Loading seg for gtm >> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz >> > Loading seg ctab >> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab >> > Reading /Users/jonathandubois/data/fssub/epc_02/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 MRTM
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.dub...@gmail.com <mailto: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 > <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: > <5609ba16.2090...@nmr.mgh.harvard.edu > <mailto: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_02/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_02/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. 0. 0. 0. 0. 0. > > 4 avail.processors, using 1 > > Creating output directory gtmpvc.output > > Loading seg for gtm > > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz > > Loading seg ctab > > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab > > Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta > > Replacing 18 > > Pruning ctab
Re: [Freesurfer] PET tools in FS dev v6.0
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_02/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_02/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. 0. 0. 0. 0. 0. > > 4 avail.processors, using 1 > > Creating output directory gtmpvc.output > > Loading seg for gtm > > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz > > Loading seg ctab > > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab > > Reading /Users/jonathandubois/data/fssub/epc_02/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 t
Re: [Freesurfer] PET tools in FS dev v6.0
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_02/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_02/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. 0. 0. 0. 0. 0. 4 avail.processors, using 1 Creating output directory gtmpvc.output Loading seg for gtm /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz Loading seg ctab /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab Reading /Users/jonathandubois/data/fssub/epc_02/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> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0 > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/li
Re: [Freesurfer] PET tools in FS dev v6.0
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_02/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_02/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. 0. 0. 0. 0. 0. > 4 avail.processors, using 1 > Creating output directory gtmpvc.output > Loading seg for gtm > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz > Loading seg ctab > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab > Reading /Users/jonathandubois/data/fssub/epc_02/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, > > > &
Re: [Freesurfer] PET tools in FS dev v6.0
Hi Doug, Thanks for sending me this information. I ran gtmseg, and bbregister successfully (I inspected both and they look accurate), but I am getting a s egfault 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_02/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_02/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. 0. 0. 0. 0. 0. 4 avail.processors, using 1 Creating output directory gtmpvc.output Loading seg for gtm /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz Loading seg ctab /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab Reading /Users/jonathandubois/data/fssub/epc_02/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> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0 > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <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 > > 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://
Re: [Freesurfer] PET tools in FS dev v6.0
Hi Jonathan just a warning that Doug is likely to be out of contact for a few days so please repost this type of question sometime next week. cheers Bruce On Wed, 23 Sep 2015, Jonathan DuBois wrote: Hi Doug, Thanks for sending me this information. 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_02/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_02/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. 0. 0. 0. 0. 0. 4 avail.processors, using 1 Creating output directory gtmpvc.output Loading seg for gtm /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz Loading seg ctab /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab Reading /Users/jonathandubois/data/fssub/epc_02/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> Subject: Re: [Freesurfer] PET tools in FS dev v6.0 To: freesurfer@nmr.mgh.harvard.edu Message-ID: <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] PET tools in FS dev v6.0
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 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.
Re: [Freesurfer] PET tools in FS dev v6.0
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 > 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.
