 |
 |
Thanks Mark, I will consider what you have said, Best, Joshua On Thu, Oct 4, 2012 at 11:56 PM, Mark Jenkinson <[log in to unmask]> wrote: > Hi, > > To start with, you can apply an anisotropic smoothing by creating a custom > kernel file. This needs to be a nifti image and will be fairly small (the > size of the non-zero kernel) and filled with whatever values you wish it to > have). We recommend that it has the same voxel size as the image you will > apply it to. You can either set-up the kernel in something like matlab, or > you could set values by hand in FSLView, or any other means. > > As for applying it to images - if it is just the same anisotropic kernel > everywhere, then that is fine. If you want to apply this within an ROI but > not elsewhere (or vary it in any other way) then you will have > non-stationary noise which causes problems for most multiple-comparison > correction techniques that assume that each voxel has been treated > equivalently. That being said, there is known non-stationary noise in the > images themselves, and so to small degrees it won't matter too much. Just > avoid really big changes - or avoid any at all and apply the same > (anisotropic) smoothing everywhere. > > I hope this helps. > All the best, > Mark > > > On 1 Oct 2012, at 22:20, Joshua Lee <[log in to unmask]> wrote: > > Thanks. > Generally, I agree that is a good idea. However, I am concerned about > using a typical scheme because in my hi-res fmri study, the adjacent > regions I am interested in are smaller than the typical smoothing kernel. > Using even 4mm smoothing kernel on the whole image would mean that > activation in region X is due to adjacent sub-region y...Further, without > smoothing, the data is noisy. > - > Josh > > On Mon, Oct 1, 2012 at 1:52 PM, Marenco, Stefano (NIH/NIMH) [E] < > [log in to unmask]> wrote: > >> Not sure ….I would apply the same procedure to the whole image… **** >> >> ** ** >> >> *Stefano Marenco, MD* >> >> NIMH/CBDB**** >> >> 10 Center Drive, Bldg 10 room 3C103**** >> >> Bethesda MD 20892**** >> >> Tel 301 435-8964**** >> >> Fax 301 480-7795**** >> >> Email: [log in to unmask]**** >> >> ** ** >> >> *From:* Joshua Lee [mailto:[log in to unmask]] >> *Sent:* Monday, October 01, 2012 4:15 PM >> *To:* [log in to unmask] >> *Subject:* Re: [FSL] Anistropic Spatial Smoothing Kernels**** >> >> ** ** >> >> Hey thanks! >> Might I ask another question? >> >> If one were to apply a standard spatial smoothing kernel to just >> subsections of a functional image through the use of masks (e.g. use a mask >> to Gaussiansmooth just one subfield of the hippocampus), would the >> resulting smoothed image be problematic for use in analyses?**** >> >> Joshua**** >> >> ** ** >> >> On Mon, Oct 1, 2012 at 8:02 AM, Marenco, Stefano (NIH/NIMH) [E] < >> [log in to unmask]> wrote:**** >> >> Afni should have something to that effect….**** >> >> **** >> >> *Stefano Marenco, MD***** >> >> NIMH/CBDB**** >> >> 10 Center Drive, Bldg 10 room 3C103**** >> >> Bethesda MD 20892**** >> >> Tel 301 435-8964**** >> >> Fax 301 480-7795**** >> >> Email: [log in to unmask]**** >> >> **** >> >> *From:* Joshua Lee [mailto:[log in to unmask]] >> *Sent:* Friday, September 28, 2012 4:15 PM >> *To:* [log in to unmask] >> *Subject:* [FSL] Anistropic Spatial Smoothing Kernels**** >> >> **** >> >> Hi all, >> I am interested in using an anistropic kernel to spatially smooth >> high-resolution functional data. For example I'd want a 8mm FWHM in the z >> direction, but only 2 mm in z and y directions. In the structure I am >> examining, this appears to be a good way of increasing SNR while retaining >> spatial localization of activations to anatomical structures. >> >> Has anyone done something like this before, and if so might I profitably >> use fslmaths to do so? >> **** >> >> -**** >> >> Josh**** >> >> **** >> >> ** ** >> > > >