Wups, yeah, forgot that bit. Nice catch. Tim
On Tue, May 20, 2014 at 3:12 PM, Ausaf Bari <aus...@gmail.com> wrote: > 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
