On Thu, Aug 3, 2017 at 9:03 AM, Claude Bajada <c.baj...@fz-juelich.de> wrote:
> 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? > Ah, I missed this question on my first read. You make a good point, that individual surfaces have some bias away from the group. With a good registration, doing this could tell you interesting things about the subject (the relative size of a particular group-identified feature on this individual). Strictly speaking, though, it will cause some bias in the display of group results, in terms of the size of features. Displaying on group average surfaces may actually have some bias too - different regions will lose different amounts of folding detail (because of differences in variability), which also means losing surface area (and therefore features in high variability regions may *look* smaller than they should on group surfaces). For processing group-average data, we compensate for this surface area loss with the use of vertex areas. I'm not entirely sure whether the surface inflation method we use tries to keep the vertex areas relatively undistorted, but if so, then the group very_inflated surfaces may have the least bias from this effect (less folding present in the surfaces before averaging, so less surface area lost due to averaging). Note that this bias would be only in visual size, not in intensity or sampling density. Back on the single-subject template topic, as a practical matter, we can't yet segment individual cerebellums into surfaces reliably, so carefully acquired and processed single subjects such as colin are the best we can do at present for displaying the cerebellum as a surface. > 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> > 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 <amy.al...@monash.edu> >> www.med.monash.edu.au/psych/bmh/ >> >> <http://www.med.monash.edu.au/psych/bmh/> >> <http://www.monash.edu/neuro-institute/> >> >> On 3 August 2017 at 07:00, Timothy Coalson <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> >>> 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 >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>> >>> >> > _______________________________________________ > HCP-Users mailing list > 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. 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