External Email - Use Caution
Thanks.
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 CautionYes. 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 surfaceor
> 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 theminto
>> 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 thestem
>> 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>
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