How can I discard the first 4 time points of each run during concatenating several runs? I know I can skip the first 4 time points with the flag -nskip 4 in configuring a analysis, but this condition can be only applicable when each run is modelled into the GLM independently, right? If I feed the mkanalysis-sess with the concatenated file, it will only skip the first 4 time points of the 1st run in this file.

In addition, if my task design is event-related, do I need to set the duration of each stimulus as 0?

Thanks and best

On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

If you just want to concatenate you can use something like
mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
002/fmcpr.up.sm5.fsaverage.lh.nii.gz
003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
all.fmcpr.up.sm5.fsaverage.lh.nii.gz

On 11/07/2018 12:30 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi Dougles,
>
> Thank your for your reply. Now I am using FSFAST, but I didn't find
> flags in prepro-sess which can be used in combing or dividing fMRI
> data. Using the following code I could get three files for each run
> (left cortical surface, right cortical surface and sub-cortical volume):
>
> /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface
> fsaverage lhrh -mni305 -fwhm 5 -per-session/
>
> Can I use preproc-sess to combine files from different runs, and
> discard the first 4 time points of each run? If so, could you please
> give me a example?
>
> Thanks and best,
>
> Zhi
>
>
> On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
> Are you using FSFAST? If you run the preprocessing
> (preproc-sess), then
> it will get you most of the way there.
>
> On 11/05/2018 10:16 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer experts,
> >
> > May I ask how can I modify the surface-based fMRI data, such as
> > combing two independent sessions into one or dividing one 4D into a
> > series of 3D surface-based fMRI files in which each one denotes a
> > single volume/TR? Thank you very much.
> >
> > Best wishes,
> >
> > Zhi
> >
> >
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