There is a bug in -cifti-correlation-gradient in 0.82 and earlier that will be fixed in the next release - if you don't specify smoothing, it will run extremely long and give the wrong answer. Specify a surface smoothing kernel of any positive size and all will be well in that command.
Tim On Thu, Aug 1, 2013 at 8:37 AM, Sebastian Urchs <[email protected]>wrote: > Hey Matt, > > thank you very much for your email. I am trying to create cifti timeseries > from non hcp data (i.e. our own data). The reason I want to do that is that > I want to use the connectome workbench -cifti-correlation-gradient command > to generate a functional connectivity gradient map and the command requires > the format. > > I have so far attempted to generate the cifti timeries > with -cifti-create-dense-timeseries using .metric files as metric inputs > (created from my 4D nifti with -metric-convert) but when I use this cifti > timeseries as input to -cifti-correlation-gradient the process keeps > running indefinitely, neither crashing nor finishing (after about 24h). > That's why I moved on to the above mentioned example that requires > .shape.gii files > > So I guess I have to extend my question: > 1) Do I need the .shape.gii file to generate a cifti timeseries from a 4D > nii to use as input to -cifti-correlation-gradient > 2) If so, how would I go about doing that? > 3) If not, what would be the correct command to run > -cifti-correlation-gradient > > Thanks a lot, > Sebastian > > > On 31 July 2013 22:34, Glasser, Matthew <[email protected]> wrote: > >> While I'm happy to explain how to do this, what is the reason you need >> to recreate this file? We do distribute these cifti timeseries already >> made and the process to make them as we have requires multiple steps, >> described at a conceptual level in: >> >> http://www.sciencedirect.com/science/article/pii/S1053811913005053 >> >> We should just be sure that recreating the dense timeseries is really >> the easiest way to accomplish whatever you are trying to do. >> >> Peace, >> >> Matt. >> >> From: Sebastian Urchs <[email protected]> >> Date: Wednesday, July 31, 2013 8:57 AM >> To: "[email protected]" <[email protected]> >> Subject: [HCP-Users] -cifti-create-dense-timeseries input question >> >> Hi all, >> >> I am trying to create a cifti timeseries from a 4D .nii file. I found >> an example for -cifti-create-dense-timeseries that uses a .shape.gii file >> as -roi-left input. I also found a corresponding shape.gii file in the hcp >> preprocessed data folder called ${SUBJECTID}.L.roi.32k_fs_LR.shape.gii. My >> question is: what is this file and how can I create it from my surface and >> nii files? >> >> Thank you very much, >> Sebastian >> >> _______________________________________________ >> 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. >> > > _______________________________________________ > 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
