Re: [HCP-Users] Creating Group Average Resting State fMRI

[Harms, Michael]

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