External Email - Use Caution I see. Thank you very much. Another question is if I can use other template for parcellation when I use recon-all?
On Tue, 23 Oct 2018 at 13:42, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You specify the input you want selxavg3-sess to use. Otherwise, it will > try to look for things that have been preprocessed. > > On 10/23/18 12:17 PM, Zhi Li wrote: > > 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 > > > > _______________________________________________ > 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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