Thanks. I will try that. -Ausaf
On Tue, May 20, 2014 at 8:25 PM, Harms, Michael <mha...@wustl.edu> wrote: > > You could do that if you just want a heuristic map of the "group > activation". But I wouldn’t use that for anything that requires meaningful > statistics. To compute "proper" Level 3 task maps what we do currently is > convert the CIFTI copes/varcopes to NIFTI, merge them into a 4D NIFTI file, > and then use those as inputs to 'flameo' in a mixed effects analysis. (And > then convert those outputs back to CIFTI). > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: Ausaf Bari <aus...@gmail.com> > Date: Tuesday, May 20, 2014 5:56 PM > To: Matt Glasser <glass...@wusm.wustl.edu> > > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI > > On a similar note, I also want to find the group average of a > particular task fMRI such as the emotion task fMRI. I found a .dscalar.nii > CIFTI file for each task for each subject. > > Can I average the .dscalar.nii files together across subjects with > cifti-average since these are just CIFTI scalars files with a z-statistic > column? > > -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. >> > > _______________________________________________ > 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
