Hi Gabriel can you give us details of your acquisition? Why is it so noisy? Bruce
On Wed, 19 Jun 2013, Gabriel Obregon wrote: > Hi Douglas, > > The brainmask volumes are extremely grainy (similar to the raw structurals), > i.e., dark voxels throughout the WM and high-intensity voxels across the > gray matter. As far as I understood, all WM voxels (unless a lesion is > present) should have a uniform intensity distribution after the > normalization stages within the volume processing pipeline. Moreover, this > makes the WM edits particularly challenging, for it's very difficult to > trace the boundaries of some of the WM strands. > > I don't know if this represents an issue but it's definitely something I > hadn't encountered before. Any input would be really appreciated! > > Thanks, > > --G > > On Jun 19, 2013, at 2:23 AM, Douglas Greve <[email protected]> > wrote: > > Hi Gabriel, I don't have experience with the MR-PET yet. Why do > you think there is a problem? Try running wm-anat-snr on this > subject. In general, you don't want to be smoothing/denoising > the anatomical > doug > > > > > > On 6/18/13 1:13 PM, [email protected] wrote: > > Hi, > > I've started segmenting several structural scans from an MR-PET study > conducted in Bay 7, and was wondering if someone has previous experience > working with MPRAGE images acquired using the MR-PET coils? > > The scans have a very low SNR and I am trying to figure out if this could > potentially affect the performance of the automated surface > reconstructions. I've scrolled through the volumes and even though the > surfaces seem normal, I am somewhat skeptical about their true quality > given that intermediate stages, such as the intensity normalization, seem > to be failing (please find an example from one of the brain masks > attached). > > Is it essential to filter the raw structurals before segmenting them, and > if so, are there any readily available denoising tools? Furthermore, are > there any additional issues I should take into consideration? > > Thanks for your help! > > Gabriel > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ Freesurfer mailing list [email protected] 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.
