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
