External Email - Use Caution I see. Thank you very much.
On Wed, 7 Nov 2018 at 15:18, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> wrote: > 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
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