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>> 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>>> > 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>> > > > 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
