Hi Mary Kate, Keep in mind that all of the HCP tasks utilize a blocked design. Consequently, they have high power for detecting activation, but low power for estimating the shape of hemodynamic responses.
If you are interested in “activation” as percent signal change, for volume statistics, you can use fslstats to extract the values from the cope##.nii.gz maps using the ROI as a mask, and then multiply by 100. If you are doing this on CIFTI data, it’s more difficult. However, I believe it ultimately involves wb_command -nifti-information with the -print-matrix option. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: [email protected] > On Feb 13, 2015, at 1:58 PM, Glasser, Matthew <[email protected]> wrote: > > Very likely, but I don’t have a clear sense of what you are wanting to do > with the data. Perhaps explaining the analysis you want to perform will lead > to an explanation of how to do it with FSL/Connectome Workbench. > > Peace, > > Matt. > > From: Mary Kate Meacham <[email protected]> > Date: Friday, February 13, 2015 at 1:57 PM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] Using MarsBar on HCP data > > Is there a method through FSL/Connectome Workbench that would serve me the > same way? > > --Mary Kate > > On Feb 13, 2015, at 1:48 PM, "Glasser, Matthew" <[email protected]> > wrote: > >> Hopefully someone out there uses SPM with HCP data and can comment, as most >> of us use FSL/Connectome Workbench. >> >> Peace, >> >> Matt. >> >> From: Mary Meacham <[email protected]> >> Date: Friday, February 13, 2015 at 1:45 PM >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] Using MarsBar on HCP data >> >> It is a region of interest (ROI) toolbox for SPM. >> http://marsbar.sourceforge.net/ >> >> Is there another toolbox or method that you would suggest I use? >> >> Best, >> Mary Kate >> >> On Fri, Feb 13, 2015 at 1:43 PM, Glasser, Matthew <[email protected]> >> wrote: >>> What is MarsBar? That sounds like a type of candy… >>> >>> Peace, >>> >>> Matt. >>> >>> From: Mary Meacham <[email protected]> >>> Date: Friday, February 13, 2015 at 1:41 PM >>> To: "[email protected]" <[email protected]> >>> Subject: [HCP-Users] Using MarsBar on HCP data >>> >>> Hi there! >>> >>> >>> I am trying to extract time series data from regions of interest for HCP >>> data. I have been advised to use MarsBar in order to do this and was just >>> wondering if anyone had any input/tips/hints/helpful information about how >>> to go about doing this? My end goal is to have timecourse data to use in >>> order to eventually find out something about the blood >>> oxygenation-level-dependent (BOLD) sginal. >>> >>> I am not too advanced in my SPM use, so any and all help and guidance is >>> appreciated! >>> >>> >>> Thank you and best wishes, >>> Mary Kate >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> 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. >> >> >> >> 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. > > > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
