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: 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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>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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