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> 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>> 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
>>
>>     _______________________________________________
>>     Freesurfer mailing list
>>     Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer