Re: [Freesurfer] Spatial smoothing kernel in fsfast

2019-05-15 Thread Zhi Li
External Email - Use Caution Thanks. On Wed, 15 May 2019 at 16:42, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Right, with -fwhm 0, it will not smooth the data. > > On 5/14/19 2:21 PM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Yes. Smoothin

Re: [Freesurfer] Spatial smoothing kernel in fsfast

2019-05-15 Thread Greve, Douglas N.,Ph.D.
Right, with -fwhm 0, it will not smooth the data. On 5/14/19 2:21 PM, Zhi Li wrote: > > External Email - Use Caution > > Yes. Smoothing in the volume may smooth across sulci and other tissue > types. I would like to use ICA-AROMA to denoise the data, especially > remove the head motion c

Re: [Freesurfer] Spatial smoothing kernel in fsfast

2019-05-14 Thread Zhi Li
External Email - Use Caution Yes. Smoothing in the volume may smooth across sulci and other tissue types. I would like to use ICA-AROMA to denoise the data, especially remove the head motion component. However, this toolbox do not support surface-based data, and according to the su

Re: [Freesurfer] Spatial smoothing kernel in fsfast

2019-05-14 Thread Greve, Douglas N.,Ph.D.
Why do you want to smooth in the volume before sampling onto the surface? That would defeat one of the main reasons to sample on the surface (ie, surface-based smoothing instead of volume-based). Volume-based smoothing in the subcortical regions is automatically done when you specify a FWHM in

Re: [Freesurfer] Spatial smoothing kernel in fsfast

2019-05-14 Thread Zhi Li
External Email - Use Caution Sorry for the confusing expression. I mean smooth on the volume before resampling volume to the three standard spaces (left and right surface and subcortical space). Anyway, I think I have figured it out. In the last two steps of 'preproc-sess', the vol

Re: [Freesurfer] Spatial smoothing kernel in fsfast

2019-05-14 Thread Greve, Douglas N.,Ph.D.
sorry, I'm not sure what you are trying to do. When you say you would like to smooth the data then resample, do you mean smooth on the surface? and do you mean resample to the standard surface or volume space? On 5/13/2019 11:26 AM, Zhi Li wrote: External Email - Use Caution Dear Frees