It isn't too hard with -cifti-reduce and -cifti-math (though it does need -select and -repeat):
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 there are places with 0 stdev in all concatenated timeseries, the correlation will probably give back NaNs, which will have to be fixed. Tim On Tue, May 20, 2014 at 2:44 PM, Glasser, Matthew <glass...@wusm.wustl.edu>wrote: > Demean and normalize functionality might be useful things to add to > wb_command -cifti-merge, unless there is a simple wb_command way to do this > already (we generally do this in matlab now). > > Matt. > > From: Timothy Coalson <tsc...@mst.edu> > Date: Tuesday, May 20, 2014 at 12:19 PM > To: Stephen Smith <st...@fmrib.ox.ac.uk> > Cc: Ausaf Bari <aus...@gmail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI > > Should you also normalize so that the standard deviations of each > timeseries match? > > Tim > > > > On Tue, May 20, 2014 at 12:24 PM, Stephen Smith <st...@fmrib.ox.ac.uk>wrote: > >> Hi - One important point - you should never temporally concatenate >> without first demeaning the individual timeseries. >> Cheers. >> >> >> >> On 20 May 2014, at 10:14, Ausaf Bari <aus...@gmail.com> wrote: >> >> Ok that is something I tried recently actually - to merge all the runs >> across all the subjects and then do a correlation with fisher-z transform. >> The results didn't "feel" right in that they didn't look like typical >> resting state images. That is why I wanted to double check I was doing it >> the right way. >> >> As an alternative could I merge the within subject runs together with >> -merge and do a within-subject correlation and then average across >> subjects? Is there any downside to this other than the huge amount of >> storage space that would be required (32GB per subject)? >> >> -Ausaf >> >> >> On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew < >> glass...@wusm.wustl.edu> wrote: >> >>> The simplest way is to concatenate the timeseries with wb_command >>> -cifti-merge. You could do this for all runs of all subjects, or all runs >>> for each subject (and then z-transform and average the connectomes across >>> subjects). There will be a better way in the future. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Timothy Coalson <tsc...@mst.edu> >>> Date: Monday, May 19, 2014 at 10:48 PM >>> To: Ausaf Bari <aus...@gmail.com> >>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI >>> >>> Averaging together timepoints does not make sense for resting state >>> data, it does not use stimuli, so there is no temporal correspondence >>> between runs or across subjects. You should do the correlation before any >>> averaging. >>> >>> I'm not sure what method our pipelines use, so I'll let someone else >>> respond as to what the recommended method is (you probably don't need to >>> correlate each file by itself, which would use up lots of disk space). >>> >>> Tim >>> >>> >>> >>> On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari <aus...@gmail.com> wrote: >>> >>>> I am trying to create a resting state fMRI average over 10 subjects to >>>> view in connectome workbench. For each HCP subject, I found the following 4 >>>> files: >>>> >>>> rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii >>>> rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii >>>> rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii >>>> rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii >>>> >>>> So for 10 subjects, I will have 40 total files. Am I correct to >>>> assume that I can use the command line tool "wb_command -cifti-average" to >>>> average over all 40 files and then "wb_command -cifti-correlation" to >>>> create a dense connectome? >>>> >>>> -Ausaf >>>> >>>> >>>> -- >>>> Ausaf A. Bari MD PhD >>>> Resident Physician >>>> UCLA Medical Center >>>> Department of Neurosurgery >>>> >>>> Email: aus...@gmail.com >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> ------------------------------ >>> >>> 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. >>> >> >> >> >> -- >> Ausaf A. Bari MD PhD >> Resident Physician >> UCLA Medical Center >> Department of Neurosurgery >> >> Phone: 617-642-1929 >> Email: aus...@gmail.com >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve >> >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net> >> >> >> >> >> _______________________________________________ >> 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 > > > ------------------------------ > > 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
