Oh, also, to reliably extract the hemisphere-specific full-surface label files: use wb_command -cifti-separate with the -label repeatable option, then load the .label.gii files it creates.
Tim On Wed, Aug 3, 2016 at 3:36 PM, Timothy Coalson <[email protected]> wrote: > First, the size of 64984 shows that the cifti file in question did not > have the medial wall masked out internally, which is likely the starting > point for these problems. I don't know how medialMask is defined, but if > it isn't 32492 elements long (in this case), then that will cause another > problem, as the break between left and right data will be in the wrong > place. > > If you really didn't do any steps between defining labelsL and labelsR, > and anotherCii was made as a copy of that same cii variable, then I don't > know how it managed to mess things up, though, unless this cifti file also > managed to have right hemisphere before left hemisphere (the format > supports this, but we have tried to be consistent with the order - the lack > of a medial wall mask indicates this dlabel file was generated in an > unusual way, though). You can use "wb_command -file-information > -no-map-info" to see the order of structures in the cifti file. > > Tim > > > On Wed, Aug 3, 2016 at 11:22 AM, Salim Arslan <[email protected]> > wrote: > >> Hello, >> >> I am trying to get Power parcellations out of >> RSN-networks.32k_fs_LR.dlabel.nii, that comes with the "Brain Analysis >> Library of Spatial maps and Atlases (BALSA) database study" ( >> https://balsa.wustl.edu/study/show/WG33). It is also part of the >> tutorial dataset. >> >> I did what I have been always doing for extracting data from CIFTI files >> in Matlab. Using ciftiopen, I obtained the cii object, which in this case, >> contains the cdata matrix of size 64984x4. The 3rd column here corresponds >> to the holes-filled Power parcellations. To extract those for both >> hemispheres, I simply split up the 64984 vector and masked out the medial >> wall vertices and then saved the labels back to CIFTI. >> >> cii = ciftiopen('RSN-networks.32k_fs_LR.dlabel.nii', wb_command); >> cdata = cii.cdata; >> parcellation = cdata(:,3); >> labelsL = cifti(1:length(medialMask)); >> labelsR = cifti(length(medialMask)+1:end); >> anotherCii.cdata = [labelsL;labelsR]; >> ciftisave(anotherCii,'power.dlabel.nii',wb_command) >> >> However when I visualized the labels on workbench, I noticed some holes >> (with random labels) in many parcels. Please see the attached figure for >> clarification. >> >> I assume this is something to do with the medial masking, but cannot >> figure out what is wrong. Any help is appreciated. >> >> Thanks for your attention. >> >> Best regards, >> Salim >> >> -- >> >> _______________________________________________ >> 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
