Hello Freesrufer Team,
I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions.
In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction.
I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L and R ROIs combined for the PVC results you reported in that paper? Or were the same 52 used for the general PVC in the FS pipeline?
Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC? Should a threshold be set for the sizes of these ROIs?
How were the white matter hypo-intensities dealt with while generating the ROI masks?
Thanks, Pradeep
Hi Pradeep
Doug is on vacation and is the best one to answer your question. If you don't get a response in a week or 10 days can you repost?
thanks Bruce On Tue, 21 Jun 2016, Pradeep wrote:
Hello Freesrufer Team,
I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions.
In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction.
I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L and R ROIs combined for the PVC results you reported in that paper? Or were the same 52 used for the general PVC in the FS pipeline?
Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC? Should a threshold be set for the sizes of these ROIs?
How were the white matter hypo-intensities dealt with while generating the ROI masks?
Thanks, Pradeep
Thank you! I will.
On Mon, Jun 20, 2016, 7:00 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Pradeep
Doug is on vacation and is the best one to answer your question. If you don't get a response in a week or 10 days can you repost?
thanks Bruce On Tue, 21 Jun 2016, Pradeep wrote:
Hello Freesrufer Team,
I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions.
In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction.
I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L
and R
ROIs combined for the PVC results you reported in that paper? Or were
the
same 52 used for the general PVC in the FS pipeline?
Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC? Should a threshold be set for the sizes of these ROIs?
How were the white matter hypo-intensities dealt with while generating
the
ROI masks?
Thanks, Pradeep
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On 06/20/2016 08:25 PM, Pradeep wrote:
Hello Freesrufer Team,
I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions.
In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction.
I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L and R ROIs combined for the PVC results you reported in that paper? Or were the same 52 used for the general PVC in the FS pipeline?
They were combined only after the PVC calculation. For the figure, I changed the GTM to show the combined GTM.
Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC?
Not sure what you mean here. You can get the variance reduction factor for each ROI in the gtm.stats.dat file. This indicates how much noise reduction you can expect (assuming gaussian noise, etc) in each ROI given the size and anatomical distribution of the ROIs and PSF.
Should a threshold be set for the sizes of these ROIs?
What do you mean?
How were the white matter hypo-intensities dealt with while generating the ROI masks?
I merged them with WM. I tried it with and without, and it did not make much of a difference. doug
Thanks, Pradeep
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks responding Doug!
I am interested us using centrum semiovale as reference region. Is there a way I can save the unsegmented white matter [5001& 5002] during the gtmseg step or what would be its equivalent label in the gtm_pvc results table?
Thanks, Pradeep
On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 06/20/2016 08:25 PM, Pradeep wrote:
Hello Freesrufer Team,
I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions.
In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by-hemisphere interaction.
I might have interpreted the Supplementary figure 1 incorrectly, but the Geometric transfer matrix seem to show around 52 ROI's, So were the L and R ROIs combined for the PVC results you reported in that paper? Or were the same 52 used for the general PVC in the FS pipeline?
They were combined only after the PVC calculation. For the figure, I changed the GTM to show the combined GTM.
Do you have any concrete results to examine the effects of the size variation over the ROIs used for PVC?
Not sure what you mean here. You can get the variance reduction factor for each ROI in the gtm.stats.dat file. This indicates how much noise reduction you can expect (assuming gaussian noise, etc) in each ROI given the size and anatomical distribution of the ROIs and PSF.
Should a threshold be set for the sizes of these ROIs?
What do you mean?
How were the white matter hypo-intensities dealt with while generating the ROI masks?
I merged them with WM. I tried it with and without, and it did not make much of a difference. doug
Thanks, Pradeep
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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