Hi Alexandra, The value stored in pixdim4 is used for a number of things, and the scripts expect them to be stored in units of seconds (e.g., 0.720 for HCP). It is used to set the TR value in the CIFTI files. Perhaps more importantly, though, it is used to determine the appropriate temporal filter parameters in the Task fMRI Analysis and FIX-ICA denoising pipelines. It is also used to set the TR in the task fMRI fsf files, which are used the the FEAT analyses.
You might be able to change the pixdim4 in the outputs of the MPP pipelines before running Task fMRI Analysis or FIX-ICA pipelines. But it’s probably easiest and safest to change them on the unprocessed NIFTI before running any HCP Pipelines. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Neuroscience Phone: 314-362-7864 Email: [email protected] > On Feb 3, 2016, at 8:37 PM, Alexandra Walton Weston <[email protected]> wrote: > > Hi all, > > I’m running non-HCP data through the HCP preprocessing pipeline. Some of our > data has niftis with the EPI TR (pixdim4) in seconds, while some data has the > TR in ms. Will having the TR in ms cause incorrect output from the HCP > preprocessing pipeline? So far we haven’t noticed anything odd, but I wanted > to make sure. > > > Alexandra Weston > Research Assistant II > Department of Behavioral Neuroscience > Fair Neuroimaging Lab > http://www.ohsu.edu/fair-lab > > [email protected] > Phone: 503 418-1894 > Fax: 503 494-9988 > > Oregon Health & Science University > Mail Code: L470 > 3181 SW Sam Jackson Park Road > Portland, OR 97239-3098 > > <image001.gif> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
