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
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
>
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