are you trying to use FSFAST to do the entire fmri anlaysis? If so, then follow the tutorial as it will handle the skipped TRs and the concatenation for you. If not, then you don't need a paradigm file
On 11/07/2018 02:14 PM, Zhi Li wrote: > > External Email - Use Caution > > Great! So I also need to subtract 8 seconds from the onset time of > each stimulus when I make the /paradigm file/, right? If the duration > of stimulus is smaller than 1 second, such as 0.05 second, do I need > to change its duration to 0 in a event-related deign? > > > On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > 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. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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. > > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> > > <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@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 > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
