External Email - Use Caution Thank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and mkanalysis-sess.
On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes. When you run mkanalysis-sess, you may still have to use the -funcstem > > On 10/23/18 10:06 AM, Zhi Li wrote: > > 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 > > > > _______________________________________________ > 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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