Re: [HCP-Users] matlab,workbench,gifti,cifti

[Glasser, Matthew]

The wb_command -cifti-convert -to-gifti-ext option is for loading the entire array into matlab. Peace, Matt. From: Colin Reveley <reve...@gmail.com> Date: Friday, October 25, 2013 6:10 PM To: Timothy Coalson <tsc...@mst.edu> Cc: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] matlab,workbench,gifti,cifti thanks. that's all most helpful. in this case the ciftis are essentially just metrics with nodes missing so the -cifti-separate worked easily. I was trying -cifti-convert before. I'm quite sure the other info will come in handy and it's all slowly building valuable insight. best Colin On 25 October 2013 19:53, Timothy Coalson <tsc...@mst.edu> wrote: Actually, there is a third way, which may be easier in this case: make a single-column cifti file from the one you have (either copy it or use -cifti-merge to select one column), and then use -cifti-replace-structure on it, with the curvature metric files.  Note, -cifti-replace-structure modifies the input cifti file, this is why you need to make a copy first. Tim On Fri, Oct 25, 2013 at 12:50 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: The two ways to do this are 1) To use wb_command -cifti-separate on your CIFTI files to separate them into GIFTI files or 2) to use wb_command -cifti-create-dense-timeseries to combine the .func.gii files (using the same medial wall ROI as for your other data). Peace, Matt. From: Colin Reveley <reve...@gmail.com> Date: Friday, October 25, 2013 12:41 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] matlab,workbench,gifti,cifti Hi -  I have a large number of .dscalar.nii files. They are surface maps. They cover every surface node, except for the medial wall.  I'm turning these into vectors and working with them in matlab. and that's great. however: I also want to analyse the relationship of these data to data that's already on the surface as func.gii (e.g. curvature) and now I have a problem since the cifti data isn't the same size as the surface. I just need the curvature (or other surface metric) to be a vector with the same length as the cifti and where the indices of the vectors represent the same nodes in both. I don't need a working cifti or gifti file, just the data as vectors of numbers in matlab. I suspect using the node indexing info in the cifti header as a guide for what metric nodes to delete (or add) is one way to go. but maybe there is a simpler way I've missed? maybe make a dscalar.nii mask of just the missing nodes and then -cifti-merge-dense that with the data (expand the cifti rather than contract gifti)? best, Colin Reveley _______________________________________________ HCP-Users mailing list 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   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