You can get cifti data into matlab fairly easily (I mention matlab because you mentioned SPM, which uses matlab), see this FAQ entry:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? Depending on how your ROIs are specified, you may need to use wb_command to do some conversion first. Tim On Fri, Feb 13, 2015 at 3:39 PM, Greg Burgess <[email protected]> wrote: > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
