To reinforce what bruce is saying, mri_surf2surf does surface-based smoothing (ie, along the cortical surface), whereas fslmaths does volume-based smoothing which does not take into account the anatomy
On 12/12/2017 10:38 AM, Bruce Fischl wrote: > 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 >> >> >> > > > _______________________________________________ > 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 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.
