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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
>>> >
>>> >
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>>
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