-cifti-convert does not do this, it only dumps the matrix into different file formats as-is, the spatial relationships are not accessible from its output.
If you are only interested in subcortical/cerebellum data, that is trivial to extract from cifti as a volumetric nifti using -cifti-separate with -volume-all. In the future, when resolution increases sufficiently, we hope to move the cerebellum data to surface representation also. Group volume-registered space has significant drawbacks, in that it does not align cortical functional areas to the degree that surface/cifti processing can. This is because much of the cortex has variable folding between subjects, which volume registration can't unfold to try to match, and because functional areas vary somewhat in their position relative to these folds. See our recent paper: https://www.ncbi.nlm.nih.gov/pubmed/29925602 This actually means that mapping the cifti data back into the volume should have better cross-subject functional correspondence than computing group maps from the original volumetric data - the drawback, however, is that the folding patterns can't be preserved (since they are different across subjects), and you will end up with a much less folded cortical ribbon with oddly sharp boundaries (and perfect correlation along the normal vector of the surface). Processing the data in cifti format will use less memory, be more correct to the nature of the data, and make it more obvious that you aren't really using a volumetric processing stream. Matlab and python both have support for reading and writing cifti files (though in matlab there isn't good support for spatial relationships), as well as a few other languages (the cifti code from workbench has been made into a c++ library, though you will also need a gifti library to make full use of spatial relationships). wb_command can do several types of spatial processing operations on cifti, and -cifti-convert will allow you to feed the data through virtually any tool that doesn't use spatial neighborhood information. Tim On Tue, Nov 13, 2018 at 10:45 AM, Nicola Toschi <tos...@med.uniroma2.it> wrote: > Thank you Steve, > > I was hoping to get them out of the CIFTI versions (also so I don't have > to reprocess the 4D FIX data for all subjects). Maybe with cifti-convert? > The brain would not be fully covered here i realise but much better than > nothing. > > Alternatively, do you think there is a chance of obtaining them somehow > (since they have been calculated by you guys anyway)? Can i put in a > request somewhere maybe? > > Thank you in advance! > > Nicola > > > On 11/13/2018 5:13 PM, Steve Smith wrote: > > Hi - we calculated them in order to estimate the volumetric group maps. > However AFAIK we didn't bundle them in the PTN release. > You can easily get them though by regressing node timeseries into 4D > FIX-cleaned data. > > Cheers. > > > On 13 Nov 2018, at 16:09, Nicola Toschi <tos...@med.uniroma2.it> wrote: > > Dear HCP list and experts, > > I was wondering if the subject-specific node maps from the latest PTN > release (which are available in CIFTI format) are also available in > volumetric space (which would aid the specific analysis we are running). > > Or if not, maybe a pointer on how to convert them? > > Thank you very much in advance! > > nicola > > --- > This email has been checked for viruses by Avast antivirus software. > https://www.avast.com/antivirus > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ------------------------------------------------------------ > --------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, WIN (FMRIB) Oxford > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 610470 > st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve > ------------------------------------------------------------ > --------------- > > Stop the cultural destruction of Tibet <http://smithinks.net> > > > > > > > > > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient&utm_term=icon> > Virus-free. > www.avast.com > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient&utm_term=link> > <#m_-1125881958447918270_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > HCP-Users mailing list > 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
