External Email - Use Caution I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing?
*preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run* If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization? On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > 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> 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 >> > 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 > listfreesur...@nmr.mgh.harvard.eduhttps://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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