Re: [Freesurfer] Segmentation of MR-PET structurals
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, obre...@nmr.mgh.harvard.edu 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 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.
Re: [Freesurfer] Segmentation of MR-PET structurals
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 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, obre...@nmr.mgh.harvard.edu 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 >> 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.
Re: [Freesurfer] Segmentation of MR-PET structurals
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 > 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, obre...@nmr.mgh.harvard.edu 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 > 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.
