On Wed, 15 May 2019 at 16:42, Greve, Douglas N.,Ph.D. <DGREVE@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. 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 suggestions in their study(
> https://www.ncbi.nlm.nih.gov/pubmed/25770991 ), ICA denoising should
> be applied after spatial smoothing and prior to temporal filtering.
> That's why I want to smooth in the volume before resampling, I set the
> flag '-fwhm' in preproc-sess as 0, hence it should not smooth the
> data, right?
>
> Best wishes,
>
> Lizhi
>
> On Tue, 14 May 2019 at 13:40, Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
> 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 preproc-sess
>
> On 5/14/19 1:02 PM, Zhi Li wrote:
> >
> >         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 volume data is first
> resampled
> > to the standard surface with 'mri_vol2surf' and volume space with
> > 'mri_vol2vol', and then smoothed on each space with 'mri_fwhm'. The
> > masks of surface and volume are applied in 'mri_fwhm', not
> > 'mri_vol2surf' nor 'mri_vol2vol'. So if the flag '-fwhm' is set
> as 0,
> > 'mri_fwhm' will not be initiated and the data will not be masked,
> > that's why I got the whole brain data in the file
> > 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I
> know
> > the command to mask the volume and surface fMRI data?
> >
> > Besides, is that correct about the second question? Thank you
> very much.
> >
> > Best wishes,
> >
> > Lizhi
> >
> >
> > On Tue, 14 May 2019 at 11:29, Greve, Douglas N.,Ph.D.
> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
> wrote:
> >
> > 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 Freesurfer experts.
> >>
> >> Now I am using preproc-sess to preprocess functional MRI
> data. I
> >> would like to smooth the data first and then resample them into
> >> the standard space. Hence I run 'preproc-sess -s sub001
> -fsd func
> >> -stc odd -fwhm 0 -per-run' first, and then
> 'spatialsmooth-sess -s
> >> sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5',
> finally
> >> 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage
> >> lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem
> >> of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the
> >> preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz'
> contains both
> >> cortical and subcortical data. If I use '-fwhm 1' this file
> only
> >> contains the subcortical area. May I know why and how to
> fix it?
> >>
> >> About each stage embedded in 'preproc-sess', if I would like
> >> replace one stage with other software/algorithms, can I just
> >> change the name of the generated file by other
> >> software/algorithms to the name of file in this stage of
> >> 'prepoc-sess', and them rerun 'preproc-sess' while keep the
> flag
> >> '-update' on? For example, if I would like to use FSL/SPM to
> >> register the functional image to structural data, can I just
> >> rename the mat-file which describes the affine registration
> >> generated by FSL/SPM to 'register.dof6.mat'?
> >>
> >> Looking forward to your kind suggestions.
> >>
> >> Thanks and best wishes,
> >>
> >> Lizhi
> >>
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