To explain further, the MSMAll registered surfaces have vertex indices matched by nearby functional features, not by their position on folding patterns. Creating a group-average MSMAll surface is essentially asking the question "for this functional feature, where is it, on average". Based on what we know of how function doesn't stay in the same place with respect to folding across subjects, and how folding patterns in different subjects can differ considerably, we know that this will have a sizable point cloud to take the average of, so we know the answer isn't going to align well to the feature in individuals, but this is okay as long as we understand this, and don't try to use the result inappropriately. Even with freesurfer or MSMSulc surface registration, there are still many folding patterns that don't really fit anywhere in the group template, so you will inevitably have a spread-out point cloud in many regions (this subject has a small extra gyrus, which falls where that subject has a sulcus, and this subject has a sulcus that turns upward instead of going straight, etc).
The issue comes when you try to use these average coordinates as if they are in good alignment with the volume data (expecting them to follow the ~2.6mm thick cortical ribbon well) - they are not, because the volume-aligned data doesn't agree on where that cortical function is across subjects - different subjects have it at different coordinates. For other types of data that are functionally relevant (for instance, fMRI), averaging by vertices across subjects using MSMAll is asking things like "for this functional feature, what is its average signal change during task X". This is perfectly fine, and is exactly the question you want to be asking. It all boils down to what you expect of the data after averaging, and how well the subject data co-locates with your registration features. Tim On Thu, Aug 3, 2017 at 9:11 AM, Harms, Michael <mha...@wustl.edu> wrote: > > > Creating an “average-surface” is fine, and we in fact to that and provide > it as part of our “group-average” data (available for download from > ConnectomDB). > > > > But, those average surfaces are just a “back-drop” for > overlaying/visualizing the metric/cifti data, and aren’t intended to be > used as a substrate for extracting coordinates. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > <(314)%20747-6173> > > St. Louis, MO 63110 Email: > mha...@wustl.edu > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Claude > Bajada <c.baj...@fz-juelich.de> > *Date: *Thursday, August 3, 2017 at 9:06 AM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] Follow-up to: Obtaining the MNI coordinates of > cluster peaks in the melodic_IC.dscalar.nii ICA maps > > > > 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> > 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/ > > > > [image: mage removed by sender.] <http://www.med.monash.edu.au/psych/bmh/> > > [image: mage removed by sender.] <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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