Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote: External Email - Use Caution Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume? On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm. On 10/22/2018 04:08 PM, Zhi Li wrote: > > External Email - Use Caution > > Hi FreeSurfer Experts, > > I am trying surface-based analysis of task-fMRI with FS-FAST. However, > I would like to apply ICA-based denoising and wavelet-despiking which > can be not done with the 'preproc-sess'. I wonder if I can do the > preprocessing with other tools before registration with FS anatomical > and normalization? If it is available, how can I do it with command line? > > Another question is if can I use other template for parcellation > during using 'recon-all', such as the template of Human Connectome > Project? > > Looking forward to your kind reply. > > Thank you and best wishes, > > Zhi > > > _______________________________________________ > 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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