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> 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:
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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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