External Email - Use Caution Got it. Thank you very much for your patient reply.
Best wishes On Tue, 23 Oct 2018 at 18:59, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > can you clarify what you mean? We produce two cortical parcellations by > default (one from Christophe Destrieux and one from Rahul Desikan). What > kind of parcellation would you want? Note that the parcellation is not > done > by propagating a template to the individual. Rather we extract an array of > statistics from a manually labeled training set and use them to parcellate > new subjects > > cheers > Bruce > > On Tue, 23 Oct 2018, Zhi Li wrote: > > > > > 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 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 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 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 list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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