1. That command for the surface is not quite what you are looking for. For the surface, the left and right hemisphere vertices are already in register (meaning that vertices with the same number will be in the anatomically corresponding location). You would need to translate between the CIFTI indices and the GIFTI surface indices to take advantage of that however. The easiest way to do this would be to use wb_command -cifti-separate and the you can do operations on the resulting GIFTI files. 2. I think if you fed wb_command -volume-resample (on the NIFTI files that result from wb_command -cifti-separate) a matrix with the form:
-1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 This might accomplish the left right flip in the volume, however Tim should confirm if he agrees. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Daria Jensen <dariajen...@gmail.com<mailto:dariajen...@gmail.com>> Date: Friday, September 1, 2017 at 11:47 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: Miriam Klein-Flugge <mklein0...@googlemail.com<mailto:mklein0...@googlemail.com>> Subject: [HCP-Users] clustering of subcortical structures - flipping and smoothing Dear HCP list, We’re interested in clustering of subcortical structures in the HCP resting-state fMRI data and have two questions regarding the pre-processing: 1. We’re looking for a way to flip the data of the two hemispheres, including subcortical structures, It seems that an option exist to do his for the surface (-surface-flip-lr). Which procedure would you recommend for flipping the hemispheres of the whole brain, including the volume data? 2. Moreover, we’re thinking of applying wb_command -cifti-smoothing to the individual dtseries files with a fwhm of 3mm for subcortical structures to make the clustering more robust. Our approach would be to smooth across subcortical boundaries. What would be your advice? Has anyone got advice with regards to the kernel size? And finally, why do we need to indicate a left and right surface file in the command? How are these files used the smoothing process (and do they have to correspond to the surface from each individual)? Thank's a lot! Daria Jensen _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
