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. 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. > > <dgr...@mgh.harvard.edu <mailto:dgr...@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. > > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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> > > <mailto: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> > > <mailto: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 <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
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