Tim - minor correction in your cifti-math formula: I think you need the <cifti-output> right after the expression.
On Tue, May 20, 2014 at 1:00 PM, Timothy Coalson <tsc...@mst.edu> wrote: > 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. >> > > -- 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
