fsl doesn't support CIFTI files yet. What you want for those is wb_command -cifti-merge:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-merge Tim On Tue, Mar 24, 2015 at 4:18 PM, Farrant, Kristafor <kxf...@miami.edu> wrote: > Thanks! > > > I should be able to use > > > > wb_command -cifti-reduce <input> MEAN mean.dtseries.nii > > wb_command -cifti-reduce <input> STDEV stdev.dtseries.nii > > wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x <input> -var > > mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii > > -select 1 1 -repeat > > > > And then concatenate the data using FSLs fslmerge? > > > Kris > > > -- > > Kristafor Farrant M.Sc. > Lab Manager (BCCL) > Department of Psychology > 5151 San Amaro Drive > Room 114 E > University of Miami > Coral Gables, FL 33124 > > Phone: 305-284-3273 > Email: kxf...@miami.edu > Website: http://www.psy.miami.edu/bccl/ <http://www.psy.miami.edu/bccl/> > ------------------------------ > *From:* Glasser, Matthew <glass...@wusm.wustl.edu> > *Sent:* Tuesday, March 24, 2015 5:14 PM > *To:* Farrant, Kristafor; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Group average rfRMI - demean, variance > normalize, concatenate OR demean, concatenate, then variance normalize? > > I would variance normalize each run prior to concatenating. I would do > this so that one is variance normalizing according to the amount of > unstructured noise in the data (meaning that one keeps differences in BOLD > variance). We’ll have some code released to help doing this hopefully soon. > > Peace, > > Matt. > > From: <Farrant>, Kristafor <kxf...@miami.edu> > Date: Tuesday, March 24, 2015 at 3:25 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Group average rfRMI - demean, variance normalize, > concatenate OR demean, concatenate, then variance normalize? > > Dear users, > > > I have recently read that you should never temporally concatenate without > first demeaning the individual timeseries, posted by Stephen Smith > > (http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00444.html). > I want to know if I should either A) demean the individual time series, > concatenate, and THEN variannce normalize or B) demean, variance normalize > and then concatenate? > > > The code available includes demeaning and variance normalization run > together: > > > > wb_command -cifti-reduce <input> MEAN mean.dtseries.nii > > wb_command -cifti-reduce <input> STDEV stdev.dtseries.nii > > wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x <input> -var > > mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii > > -select 1 1 -repeat > > > If it is the case that I should demean, concatenate and then variance > normalize, would somebody be kind enough to update the command above. > > > > Many thanks, > > > Kris > > > > > > -- > > Kristafor Farrant M.Sc. > Lab Manager (BCCL) > Department of Psychology > 5151 San Amaro Drive > Room 114 E > University of Miami > Coral Gables, FL 33124 > > Phone: 305-284-3273 > Email: kxf...@miami.edu > Website: http://www.psy.miami.edu/bccl/ <http://www.psy.miami.edu/bccl/> > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
