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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
