You have to sample the volumetric PET data onto the surface (mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).
On 12/12/2017 11:23 AM, John Anderson wrote: > Dear Dr Bruce, I highly appreciate the response. > I want to smooth PET volumetric images, when I use "fslmaths", it > shifts the signal from the cortex to the underlying structures. I > think (depending on wiki) that Freesurfer handles this issue by > smoothing on sphere. Which is the recommendded stream in PETsurfer. > > I am wondering if there are any commands within Freesurfer that can be > used to smooth volumtric PET images without taking the average signal > of the neighboring voxels (like in Gaussian smoothing). > > Also, I have question about mri_fwhm: > what is the difference between the flags (--smooth-only; --fwhm). I am > aware that "mri_fwhm" is very well explained in FS wiki, but I was > unable to exactly understand the difference. For instance when I use > the flag --smooth-only the output image is somehow similar to the > input image. Is Gaussian in this cases ~1 mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM but I extended it to be able to apply smoothing (--fwhm) as well as measure the smoothness. The --smooth-only says to not do the FWHM estimate (just smooth it). > > Thanks in advance! > J > > > > > > >> -------- Original Message -------- >> Subject: Re: [Freesurfer] cortical thickness smoothing >> Local Time: December 12, 2017 10:38 AM >> UTC Time: December 12, 2017 3:38 PM >> From: fis...@nmr.mgh.harvard.edu >> To: John Anderson <john.ande...@protonmail.com>, Freesurfer support >> list <freesurfer@nmr.mgh.harvard.edu> >> >> Hi John >> >> I don't think fslmaths takes a surface topology so they won't be the same >> (mri_surf2surf smooths within the surface and fslmaths smooths in the >> volume I believe) >> >> cheers >> Bruce >> >> >> On Tue, 12 Dec 2017, John Anderson wrote: >> >> Dear Freesurfer experts, >> I ran recon-all with the flag -qcache to generate smoothed >> cortical thickness maps. >> In order to check how the flag "-qcache" is smoothing the >> cortical thickness data. I looked into the >> file $subj_dir/scripts/recon-all.log" which showed that the >> following command was applied: >> mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval >> lh.sulc.fsaverage.mgh --tval >> lh.sulc.fwhm5.fsaverage.mgh --cortex >> Please I want to know whether the flag "--fwhm" applies similar >> smoothing method to the smoothing >> output of the command "fslmaths": >> fslmaths <input_image.nii> -kernel gauss 2.213 -fmean >> <output_image.nii> -odt float >> I want to smooth two different modality-images using the cortical >> thickness smoothing method. >> Thank you for any advice! >> John >> >> >> >> 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
