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Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
External Email - Use Caution
Hi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.commailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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Hi Douglas,
Could you answer to my previous request ?
Best, Matt
Le 21 déc. 2018 à 20:22, Matthieu Vanhoutte matthieuvanhoutte@gmail.com a écrit :
Hi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.commailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): *mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc*
If I omitted *--rbv *or* --mgx* option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ?
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ? Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.commailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Douglas,
Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ? 2) Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionI used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ?
Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Douglas,
Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ? It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces. 2) Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ? After
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ? Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.commailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas,
Please find comments inline below.
best, Matthieu
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. DGREVE@MGH.HARVARD.EDU a écrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Could you precise me:
- Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
- Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?
After
Thank you for this clarification. But do you use mean PET signal inside the reference region after the PVE correction, since in the particular case of pons there is no PVE correction applied to white matter ?
Do you see any objection whether intensity normalization was done before PVE correction based on the mean PET signal inside the reference region ?
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionI used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ?
Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Could you precise me:
- Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?
- Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?
After
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionI used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ?
Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
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If you intend to use one of the aseg structures, then they are the same.
On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Douglas,
Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ? It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?
2) Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ? After
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ? Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit : You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.commailto:matthieuvanhoutte@gmail.com> a écrit : Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
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External Email - Use Caution
Hi Douglas,
In order to apply intensity normalization to non-PVC PET images based on mean intensity from reference region in gtmseg.mgz, is it better to realign & reslice PET image onto gtmseg space or the reverse way ? How is it done when dealing with PVC images using gtmpvc command ?
I would like to avoid too many reslicing operations before volume to surface projection, how would you deal with it ?
Best, Matthieu
Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
If you intend to use one of the aseg structures, then they are the same.
On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Could you precise me:
- Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?
- Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?
After
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionI used the following command to obtain only rescaled voxel-wise PET image (with no PVC): mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc
If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ?
Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > Hi Douglas, > > Thanks for helping. > > To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx. > > Do you know why ? > > Best, > Matthieu > > > Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : > You will need to set --psf 0 and --no-tfe to fully turn off PVC. > > On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Hi Douglas, >> >> Could you help me on this point ? >> >> Best, >> Matthieu >> >> >> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit : >> Dear Douglas, >> >> Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ? >> >> Best, >> Matthieu >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Hi Douglas,
Could you answer to my previous question ?
Best, Matthieu
Le 30 janv. 2019 à 14:48, Matthieu Vanhoutte matthieuvanhoutte@gmail.com a écrit :
Hi Douglas,
In order to apply intensity normalization to non-PVC PET images based on mean intensity from reference region in gtmseg.mgz, is it better to realign & reslice PET image onto gtmseg space or the reverse way ? How is it done when dealing with PVC images using gtmpvc command ?
I would like to avoid too many reslicing operations before volume to surface projection, how would you deal with it ?
Best, Matthieu
Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
If you intend to use one of the aseg structures, then they are the same.
On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Could you precise me:
- Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?
- Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?
After
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > > I used the following command to obtain only rescaled voxel-wise PET image (with no PVC): > mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc > > If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ? Yes > > Best, > Matt > > Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : > I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work? > > On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Hi Douglas, >> >> Thanks for helping. >> >> To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx. >> >> Do you know why ? >> >> Best, >> Matthieu >> >> >> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit : >> You will need to set --psf 0 and --no-tfe to fully turn off PVC. >> >> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> Hi Douglas, >>> >>> Could you help me on this point ? >>> >>> Best, >>> Matthieu >>> >>> >>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit : >>> Dear Douglas, >>> >>> Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ? >>> >>> Best, >>> Matthieu >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Hello experts,
Anyone would have an advice on my previous questions ?
Best, Matthieu
Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas,
In order to apply intensity normalization to non-PVC PET images based on mean intensity from reference region in gtmseg.mgz, is it better to realign & reslice PET image onto gtmseg space or the reverse way ? How is it done when dealing with PVC images using gtmpvc command ?
I would like to avoid too many reslicing operations before volume to surface projection, how would you deal with it ?
Best, Matthieu
Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
If you intend to use one of the aseg structures, then they are the same.
On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Could you precise me:
- Is the intensity rescaling of PET image included in the mri_gtmpvc
command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?
- Is this rescaling applied before PVE correction or after (i.e. based on
PVE corrected reference region’s mean intensity) ?
After
Many thanks in advance for helping.
Best, Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionI used the following command to obtain only rescaled voxel-wise PET image (with no PVC): *mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc*
If I omitted *--rbv *or* --mgx* option I didn't get the rescaled voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise PET image (without PVC) just by dividing each voxel of the native PET image by the mean of the reference region ?
Yes
Best, Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing RBV and MGX? What is your command line? What do you mean that these options don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Thanks for helping.
To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx.
Do you know why ?
Best, Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.
On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me on this point ?
Best, Matthieu
Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Dear Douglas,
Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ?
Best, Matthieu
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Do you mean the mean intensity not corrected for PVC? I would just run mri_gtmpvc with --psf 0 --no-tfe to turn off PVC
On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hello experts,
Anyone would have an advice on my previous questions ?
Best, Matthieu
Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas, In order to apply intensity normalization to non-PVC PET images based on mean intensity from reference region in gtmseg.mgz, is it better to realign & reslice PET image onto gtmseg space or the reverse way ? How is it done when dealing with PVC images using gtmpvc command ? I would like to avoid too many reslicing operations before volume to surface projection, how would you deal with it ? Best, MatthieuLe 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit : If you intend to use one of the aseg structures, then they are the same. On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:External Email - Use Caution Hi Douglas,Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit : On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:External Email - Use Caution Dear Douglas, Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ?It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?2) Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?AfterMany thanks in advance for helping. Best, MatthieuLe 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit : On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:> > External Email - Use Caution > > > I used the following command to obtain only rescaled > voxel-wise PET image (with no PVC): > /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta > --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge > --auto-mask PSF .01 --rbv --o nopvc/ > > If I omitted/--rbv/or/--mgx/option//I didn't get the > rescaled voxel-wise PET image (without PVC). Could I obtain > the rescaled voxel-wise PET image (without PVC) just by > dividing each voxel of the native PET image by the mean of > the reference region ? Yes > > Best, > Matt > > Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a > écrit : > > I'm not sure what you mean. If you are turning off PVC, > why are you computing RBV and MGX? What is your command > line? What do you mean that these options don't seem to > work? > > On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: >> >> External Email - Use Caution >> >> Hi Douglas, >> >> Thanks for helping. >> >> To have an only rescaled voxel-wise PET image, these >> options seem to work only when -rbv method is used and >> not -mgx. >> >> Do you know why ? >> >> Best, >> Matthieu >> >> >> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu> a écrit : >> >> You will need to set --psf 0 and --no-tfe to fully >> turn off PVC. >> >> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: >>> >>> External Email - Use Caution >>> >>> Hi Douglas, >>> >>> Could you help me on this point ? >>> >>> Best, >>> Matthieu >>> >>> >>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte >>> <matthieuvanhoutte@gmail.com >>> mailto:matthieuvanhoutte@gmail.com> a écrit : >>> >>> Dear Douglas, >>> >>> Is it possible to use mri_gtmpvc command in >>> order to intensity normalize PET images >>> without applying PVE correction by setting >>> --psf to 0 ? >>> >>> Best, >>> Matthieu >>> >>> >>> >>> _______________________________________________ >>> 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 >> 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 > > _______________________________________________ > 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 mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes that's what I mean. But does this command provide an intensity normalized voxel-wise image ?
Could you explain me the realign & reslice steps from the native PET to the voxel-wise PVC PET for MGX ans RBV ?
Best, Matthieu
Le jeu. 7 févr. 2019 à 23:06, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
Do you mean the mean intensity not corrected for PVC? I would just run mri_gtmpvc with --psf 0 --no-tfe to turn off PVC
On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHello experts,
Anyone would have an advice on my previous questions ?
Best, Matthieu
Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas, In order to apply intensity normalization to non-PVC PET images based on mean intensity from reference region in gtmseg.mgz, is it better to realign & reslice PET image onto gtmseg space or the reverse way ? How is it done when dealing with PVC images using gtmpvc command ? I would like to avoid too many reslicing operations before volume to surface projection, how would you deal with it ? Best, MatthieuLe 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit : If you intend to use one of the aseg structures, then they are the same. On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:External Email - Use Caution Hi Douglas,Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit:
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:External Email - Use Caution Dear Douglas, Could you precise me: 1) Is the intensity rescaling of PET image included in the mri_gtmpvc command based on reference region in gtmseg.mgz file rather than aseg.mgz ?It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?2) Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ?AfterMany thanks in advance for helping. Best, Matthieu> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a > écrit : > > > > On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote: >> >> External Email - Use Caution >> >> >> I used the following command to obtain only rescaled >> voxel-wise PET image (with no PVC): >> /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta >> --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge >> --auto-mask PSF .01 --rbv --o nopvc/ >> >> If I omitted/--rbv/or/--mgx/option//I didn't get the >> rescaled voxel-wise PET image (without PVC). Could I obtain >> the rescaled voxel-wise PET image (without PVC) just by >> dividing each voxel of the native PET image by the mean of >> the reference region ? > Yes >> >> Best, >> Matt >> >> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a >> écrit : >> >> I'm not sure what you mean. If you are turning off PVC, >> why are you computing RBV and MGX? What is your command >> line? What do you mean that these options don't seem to >> work? >> >> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: >>> >>> External Email - Use Caution >>> >>> Hi Douglas, >>> >>> Thanks for helping. >>> >>> To have an only rescaled voxel-wise PET image, these >>> options seem to work only when -rbv method is used and >>> not -mgx. >>> >>> Do you know why ? >>> >>> Best, >>> Matthieu >>> >>> >>> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> a écrit : >>> >>> You will need to set --psf 0 and --no-tfe to fully >>> turn off PVC. >>> >>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi Douglas, >>>> >>>> Could you help me on this point ? >>>> >>>> Best, >>>> Matthieu >>>> >>>> >>>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte >>>> <matthieuvanhoutte@gmail.com >>>> mailto:matthieuvanhoutte@gmail.com> a écrit : >>>> >>>> Dear Douglas, >>>> >>>> Is it possible to use mri_gtmpvc command in >>>> order to intensity normalize PET images >>>> without applying PVE correction by setting >>>> --psf to 0 ? >>>> >>>> Best, >>>> Matthieu >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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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Hi Douglas,
Any advice ?
Best.
Le jeu. 7 févr. 2019 à 23:12, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Yes that's what I mean. But does this command provide an intensity normalized voxel-wise image ?
Could you explain me the realign & reslice steps from the native PET to the voxel-wise PVC PET for MGX ans RBV ?
Best, Matthieu
Le jeu. 7 févr. 2019 à 23:06, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
Do you mean the mean intensity not corrected for PVC? I would just run mri_gtmpvc with --psf 0 --no-tfe to turn off PVC
On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionHello experts,
Anyone would have an advice on my previous questions ?
Best, Matthieu
Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas, In order to apply intensity normalization to non-PVC PET images based on mean intensity from reference region in gtmseg.mgz, is it better to realign & reslice PET image onto gtmseg space or the reverse way ? How is it done when dealing with PVC images using gtmpvc command ? I would like to avoid too many reslicing operations before volume to surface projection, how would you deal with it ? Best, MatthieuLe 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit : If you intend to use one of the aseg structures, then they are the same. On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:External Email - Use Caution Hi Douglas,Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> aécrit :
On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:> > External Email - Use Caution > > Dear Douglas, > > Could you precise me: > 1) Is the intensity rescaling of PET image included in the > mri_gtmpvc command based on reference region in gtmseg.mgz > file rather than aseg.mgz ? It depends. If you are using pons, then that is not part of the aseg and is generated as part of the creation of gtmseg. But most of the rest of gtmseg is derived from the aseg and surfaces.
Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean intensity ?> 2) Is this rescaling applied before PVE correction or after > (i.e. based on PVE corrected reference region’s mean intensity)
?
After> > Many thanks in advance for helping. > > Best, > Matthieu > >> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a >> écrit : >> >> >> >> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote: >>> >>> External Email - Use Caution >>> >>> >>> I used the following command to obtain only rescaled >>> voxel-wise PET image (with no PVC): >>> /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta >>> --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge >>> --auto-mask PSF .01 --rbv --o nopvc/ >>> >>> If I omitted/--rbv/or/--mgx/option//I didn't get the >>> rescaled voxel-wise PET image (without PVC). Could I obtain >>> the rescaled voxel-wise PET image (without PVC) just by >>> dividing each voxel of the native PET image by the mean of >>> the reference region ? >> Yes >>> >>> Best, >>> Matt >>> >>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a >>> écrit : >>> >>> I'm not sure what you mean. If you are turning off PVC, >>> why are you computing RBV and MGX? What is your command >>> line? What do you mean that these options don't seem to >>> work? >>> >>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi Douglas, >>>> >>>> Thanks for helping. >>>> >>>> To have an only rescaled voxel-wise PET image, these >>>> options seem to work only when -rbv method is used and >>>> not -mgx. >>>> >>>> Do you know why ? >>>> >>>> Best, >>>> Matthieu >>>> >>>> >>>> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. >>>> <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu> a écrit : >>>> >>>> You will need to set --psf 0 and --no-tfe to fully >>>> turn off PVC. >>>> >>>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi Douglas, >>>>> >>>>> Could you help me on this point ? >>>>> >>>>> Best, >>>>> Matthieu >>>>> >>>>> >>>>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte >>>>> <matthieuvanhoutte@gmail.com >>>>> mailto:matthieuvanhoutte@gmail.com> a écrit : >>>>> >>>>> Dear Douglas, >>>>> >>>>> Is it possible to use mri_gtmpvc command in >>>>> order to intensity normalize PET images >>>>> without applying PVE correction by setting >>>>> --psf to 0 ? >>>>> >>>>> Best, >>>>> Matthieu >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>>
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>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
>>>>
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Greve, Douglas N.,Ph.D. -
Greve, Douglas N.,Ph.D.
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Matthieu Vanhoutte