First run
mri_convert --nskip 4
fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
then concat the skip files


On 11/07/2018 01:42 PM, Zhi Li wrote:
>
>         External Email - Use Caution
>
> 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 <mailto: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>
>     <mailto: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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