You can, but this is usually only done for display purposes (eg, you want to show the surface data in the volume along with the subcortical data). Usually, we do three separate analyses: left hemi, right hemi, and subcortical, smoothing each one in the appropriate way.Dear Dr Greve thank you so much for the advice.
Kindly, I have one addition question and I highly appreciate your feedback!
Smoothing on surface is very interesting and it is really more accurate than applying the Gaussian smoothing directly on volumetric images. I don't see any aggressive shifts in the signal when I smooth on surface! In this context, I want to know if the following procedure is legitimate:
To smooth PET volumetric images. I am thinking of using "mri_vol2surf" to sample and smooth the PET images on surface. Can I then use "mri_surf2vol" to move the smoothed images on surface to volume. How about the subcortical regions- is the smoothing on surface applicable for the whole brain, or just for the regions between pial/white?
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: fischl@nmr.mgh.harvard.edu
>> To: John Anderson <John.anderso@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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