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. <DGREVE@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. <DGREVE@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.
> <DGREVE@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.
> <DGREVE@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
>       >
>       >
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