Yes. When you run mkanalysis-sess, you may still have to use the -funcstem

On 10/23/18 10:06 AM, Zhi Li wrote:

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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:

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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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> Freesurfer@nmr.mgh.harvard.edu
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