Its in PET native space.
On Wed, Aug 10, 2016 at 2:55 PM Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
which "native" space? the pet native? the anatomical native?
On 08/09/2016 05:46 PM, Pradeep wrote:
Hello Doug,
The aux/seg.nii image which has all the ROI's defined does not seem to be in the subject's native space or the CVS template space.
How do I bring it to the subjects native space?
Thanks, Pradeep
Screenshot from 2016-08-09 14:42:10.png
On Tue, Jul 19, 2016 at 5:03 PM Pradeep <tpradeep@gmail.com mailto:tpradeep@gmail.com> wrote:
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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/