Thanks!
I should be able to use > 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? And then concatenate the data using FSLs fslmerge? Kris -- Kristafor Farrant M.Sc. Lab Manager (BCCL) Department of Psychology 5151 San Amaro Drive Room 114 E University of Miami Coral Gables, FL 33124 Phone: 305-284-3273 Email: kxf...@miami.edu Website: http://www.psy.miami.edu/bccl/<http://www.psy.miami.edu/bccl/> ________________________________ From: Glasser, Matthew <glass...@wusm.wustl.edu> Sent: Tuesday, March 24, 2015 5:14 PM To: Farrant, Kristafor; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Group average rfRMI - demean, variance normalize, concatenate OR demean, concatenate, then variance normalize? I would variance normalize each run prior to concatenating. I would do this so that one is variance normalizing according to the amount of unstructured noise in the data (meaning that one keeps differences in BOLD variance). We'll have some code released to help doing this hopefully soon. Peace, Matt. From: <Farrant>, Kristafor <kxf...@miami.edu<mailto:kxf...@miami.edu>> Date: Tuesday, March 24, 2015 at 3:25 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Group average rfRMI - demean, variance normalize, concatenate OR demean, concatenate, then variance normalize? Dear users, I have recently read that you should never temporally concatenate without first demeaning the individual timeseries, posted by Stephen Smith? (http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00444.html). I want to know if I should either A) demean the individual time series, concatenate, and THEN variannce normalize or B) demean, variance normalize and then concatenate? The code available includes demeaning and variance normalization run together: > 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 it is the case that I should demean, concatenate and then variance normalize, would somebody be kind enough to update the command above. Many thanks, Kris -- Kristafor Farrant M.Sc. Lab Manager (BCCL) Department of Psychology 5151 San Amaro Drive Room 114 E University of Miami Coral Gables, FL 33124 Phone: 305-284-3273 Email: kxf...@miami.edu<mailto:kxf...@miami.edu> Website: http://www.psy.miami.edu/bccl/<http://www.psy.miami.edu/bccl/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
