Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
Best,
Mohamed
On 26/10/15 13:27, Bruce Fischl wrote:
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed _______________________________________________ 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/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.
Hi Mohamed
do you mean for PET analysis or for the recent paper that Rebecca Shafee wrote on e.g. tissue intensity properties?
cheers Bruce
On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
Best,
Mohamed
On 26/10/15 13:27, Bruce Fischl wrote:
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed _______________________________________________ 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/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.
Hi Bruce,
Yes, for PET analysis.
Best,
Mohamed
On 26/10/15 14:45, Bruce Fischl wrote:
Hi Mohamed
do you mean for PET analysis or for the recent paper that Rebecca Shafee wrote on e.g. tissue intensity properties?
cheers Bruce
On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
Best,
Mohamed
On 26/10/15 13:27, Bruce Fischl wrote:
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed _______________________________________________ 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/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
oh, then I'll leave it for Doug Bruce On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Hi Bruce,
Yes, for PET analysis.
Best,
Mohamed
On 26/10/15 14:45, Bruce Fischl wrote:
Hi Mohamed
do you mean for PET analysis or for the recent paper that Rebecca Shafee wrote on e.g. tissue intensity properties?
cheers Bruce
On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
Best,
Mohamed
On 26/10/15 13:27, Bruce Fischl wrote:
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed _______________________________________________ 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/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
Dear Bruce,
Am I missed the answer of Dr. Greve about the following questions?
Is it possible to tell what are the implemented methods for the PET pve correction? and how we can obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?
Many thanks,
Mohamed
On 26/10/15 14:52, Bruce Fischl wrote:
oh, then I'll leave it for Doug Bruce On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Hi Bruce,
Yes, for PET analysis.
Best,
Mohamed
On 26/10/15 14:45, Bruce Fischl wrote:
Hi Mohamed
do you mean for PET analysis or for the recent paper that Rebecca Shafee wrote on e.g. tissue intensity properties?
cheers Bruce
On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
Best,
Mohamed
On 26/10/15 13:27, Bruce Fischl wrote:
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
Dear FreeSurfer Experts,
Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
Many thanks in advance,
Best,
Mohamed _______________________________________________ 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/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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mohamed, sorry, I have not fully documented the procedure yet. I've put some notes below doug
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
On 10/27/2015 04:47 PM, Mohamed Ali Bahri wrote:
Dear Bruce,
Am I missed the answer of Dr. Greve about the following questions?
Is it possible to tell what are the implemented methods for the PET pve correction? and how we can obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?
Many thanks,
Mohamed
On 26/10/15 14:52, Bruce Fischl wrote:
oh, then I'll leave it for Doug Bruce On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Hi Bruce,
Yes, for PET analysis.
Best,
Mohamed
On 26/10/15 14:45, Bruce Fischl wrote:
Hi Mohamed
do you mean for PET analysis or for the recent paper that Rebecca Shafee wrote on e.g. tissue intensity properties?
cheers Bruce
On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
Is it possible to tell what are the implemented methods? and how we can obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
Best,
Mohamed
On 26/10/15 13:27, Bruce Fischl wrote:
no, sorry, we haven't had time to document it On Mon, 26 Oct 2015, m.bahri@ulg.ac.be wrote:
> Dear FreeSurfer Experts, > > Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6? > > Many thanks in advance, > > Best, > > Mohamed > _______________________________________________ > 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/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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
m.bahri＠ulg.ac.be -
Mohamed Ali Bahri