Hi all, I am starting a new thread because while my question is related to the one ask, it is tangential.
Can I confirm that what you mean by not averaging surfaces is that one should not average the vertex points across gifti surfaces to create a so-called "average surface" Can I ask then, is averaging the data associated with vertices from individual subjects and plotting the result on a template surface (eg colin or a just using an individual as a template) also problematic? Regards, Claude On 03.08.2017 02:05, Timothy Coalson wrote: On Wed, Aug 2, 2017 at 6:02 PM, James Morrow <james.mor...@monash.edu<mailto:james.mor...@monash.edu>> wrote: Thanks Tim and Matt for the detailed responses. I agree that mapping to volumes is sub-optimal. Our goal is to identify coords to be used as targets for brain stimulation with TMS. We need MNI coords for neuronavigation. Given the extent of the TMS field, we have some tolerance for imprecisions in the mapping. I see. We generally get asked these questions in the context of fMRI analysis, hence our reluctance. How does the neuronavigation go from MNI coordinates to subject coordinates, do you happen to have a reasonable T1w MRI scan of your subjects? I don't know how big the TMS field is, and I hadn't looked at the distance from subject to group average surfaces before, but in one of the HCP subjects, I got a maximum of 2cm distance from the group average surface (using midthickness surfaces), which occurred in a few specific locations, while 90% of the surface was 1cm distance or less. Can I clarify – was the ICA run on the volumes and then later mapped on to surfaces, or was it performed on the surface data? If the former, are the original volumetric results for the ICA of each subject available anywhere in .nii format? Cheers, James James Morrow Research assistant Brain & Mental Health Laboratory Monash Institute of Cognitive and Clinical Neurosciences School of Psychological Sciences Monash University c/o MBI, 770 Blackburn Road Clayton VIC 3800 Australia T: 03 9902 9768 E: james.mor...@monash.edu<mailto:amy.al...@monash.edu> www.med.monash.edu.au/psych/bmh/<http://www.med.monash.edu.au/psych/bmh/> [http://www.med.monash.edu.au/assets/images/psych/bmh/bannerbmh.jpg]<http://www.med.monash.edu.au/psych/bmh/> [http://med.monash.edu.au/psych/email-sig/miccn-email-sig.jpg]<http://www.monash.edu/neuro-institute/> On 3 August 2017 at 07:00, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: As Matt said, "MNI coordinates" of functionally-aligned cortical surface features don't have much meaning, similar to how T1w-aligned MNI space volumes don't have good cortical functional alignment (except in a few low-variability regions). We have shown that group average surface coordinates do not follow the MNI cortical ribbon (see attached image that simply shows the average white and pial contours on top of the MNI nonlinear template). The ICA maps themselves are also more informative than just the vertices at their peaks. Surface group results should not be turned into volumetric files, group average surfaces do not have much folding left in them, and as such they do not match the MNI template anymore - this is due to folding incompatibilities between subjects, but also due to using functional surface registration instead of folding patterns. Using the individual surfaces to map to the volume and then averaging across them would spread your data out just as badly as doing volume-based analysis of cortex, so this is also highly discouraged. Despite strongly advising you not to do what you outlined, I will tell you what commands you would need. The -cifti-extrema command will output a map with 1s and -1s at each local extrema. The surface it uses is for neighbor information and distance computation - this isn't as critical as coordinates are, as it merely sets the maximum possible density of extrema (what you could get from a very noisy map). You will need to use a threshold or other method to exclude local extrema that are outside the high-valued area. We use midthickness surfaces for this kind of thing (and when doing some important spatial operation, we use corrected vertex areas to compensate for the loss of folding in group average surfaces, see -metric-smoothing). You can extract the coordinates of a surface file with -surface-coordinates-to-metric, and you can use -cifti-separate on the -cifti-extrema result to get those as metric files, so that the indices will match, so that you can use them in matlab or some other tool for ad-hoc analysis (alternatively, use -cifti-create-dense-from-template to put the surface coordinates into a cifti file). Since we advise not to do this with any group data, you are on your own here (finding the coordinates in a bunch of individuals and averaging those will give exactly the same bad answer, reflecting the fact that many/most functional areas have notably different MNI coordinates in each individual). Tim On Tue, Aug 1, 2017 at 7:46 PM, James Morrow <james.mor...@monash.edu<mailto:james.mor...@monash.edu>> wrote: Hi, We have recently downloaded the HCP900 Parcellation + Timeseries + Netmats (820 Subjects) dataset. We would like to obtain the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps. Is there any way to do this? Is the –cifti-extrema function of wb_command the correct command? It requires a surface file, but I’m not sure which would be most appropriate for the group ICA results. Alternatively, would there be a way to convert the dscalar file into a standard volumetric nii so that I can use standard FSL tools? Thanks James Morrow _______________________________________________ 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. 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