Spherical coordinates (latitude and longitude) concisely encode precise locations on an atlas surface and on individuals registered to the atlas in a way that respects cortical surface topology. Thus, they have inherent advantages over conventional stereotaxic coordinates in the context of the current thread.
Spherical coordinates were proposed years ago by my lab (https://www.pnas.org/content/95/3/788; https://www.sciencedirect.com/science/article/pii/S0042698901000451) and by Fischl et al. (https://www.sciencedirect.com/science/article/pii/S1053811998903962). Reporting locations using latitude and longitude has yet to become routine practice in neuroimaging - but it’s not too late to start! David > On Apr 25, 2019, at 9:33 AM, Joseph Orr <joseph....@tamu.edu> wrote: > > Thanks for all the input on this, its been helpful. > -- > Joseph M. Orr, Ph.D. > Assistant Professor > Department of Psychological and Brain Sciences > Texas A&M Institute for Neuroscience > Texas A&M University > College Station, TX > > > On Wed, Apr 24, 2019 at 7:34 PM Glasser, Matthew <glass...@wustl.edu > <mailto:glass...@wustl.edu>> wrote: > I do not report MNI coordinates for any studies because I don’t think they > add a lot of value for the reasons described in Tim’s PNAS paper. Studies > that provide actual results on the surface are much more useful, and I have > extensively used such studies to make incisive neuroanatomical comparisons. > I’ve also yet to be asked to provide MNI coordinates by a peer reviewer. I > think if you share the actual data, MNI coordinates are superfluous and if > you use a well defined neuroanatomical parcellation such as the HCP’s > multi-modal parcellation, it is fine to talk about findings in particular > brain areas (if you actually check to see that your findings overlap with the > brain areas you name—i.e. don’t just eyeball vs a picture on the wall). > > Matt. > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson > <tsc...@mst.edu <mailto:tsc...@mst.edu>> > Date: Wednesday, April 24, 2019 at 1:47 PM > To: Joseph Orr <joseph....@tamu.edu <mailto:joseph....@tamu.edu>> > Cc: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] "activation" tables for reporting pscalar results > > We recommend sharing the results as data files (as mentioned, this is the > intent of BALSA), even if you choose to report MNI coordinates in the text. > Something to keep in mind is that group average surfaces do not behave like > group average volume data, the surface gets smoothed out wherever folding > patterns aren't fully aligned, resulting in a surface that does not approach > gyral crowns or sulcal fundi (most notably with functional alignment such as > MSMAll - freesurfer-aligned surfaces will average to something with more > folding preserved, at the cost of functional locality, but there are still > locations with high variability in folding patterns across subjects that will > still get smoothed out on a group average surface). See supplementary > material, figure S1, and figure S9 panel B2, from our paper on the effects of > volume-based methods: > > https://www.ncbi.nlm.nih.gov/pubmed/29925602 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_29925602&d=DwMF-g&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=V2M2j6_J4Jw1xT-p6MbHM2KfzaG3vxPBvw0qdEhQjDw&s=LNy-k18zyTDL2OKMkmruNVup_vB_2K7-GD-oaRBckfk&e=> > > If meta analysis of this sort is only intended to give a very rough idea of > location, even this may not be a deal breaker. You can use wb_command > -surface-coordinates-to-metric to get the coordinates as data, use > -cifti-create-dense-from-template to convert that to cifti, and then use > -cifti-parcellate on that to get center of gravity coordinates of the > vertices used. Note that these center of gravity coordinates could be a > distance away from the surface, due to curvature. > > Tim > > > On Wed, Apr 24, 2019 at 11:06 AM Joseph Orr <joseph....@tamu.edu > <mailto:joseph....@tamu.edu>> wrote: > True - these kind of tools generally assume certain degrees of smoothing, > which isn't the case with surface-based. And activation based meta-analysis > will apply a kernel that will likely extend outside the brain for a surface > activation that is not within a sulcus. I'd be curious to hear what those > more familiar with meta-analytic methods think about how surface-based > results can be incorporated with volumetric results. > -- > Joseph M. Orr, Ph.D. > Assistant Professor > Department of Psychological and Brain Sciences > Texas A&M Institute for Neuroscience > Texas A&M University > College Station, TX > > > On Wed, Apr 24, 2019 at 11:00 AM Harms, Michael <mha...@wustl.edu > <mailto:mha...@wustl.edu>> wrote: > > > Well, that raises the question if surface-based results should just be > automatically “lumped in” with volume-based results by tools such as > neurosynth to begin with… > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > <mailto:mha...@wustl.edu> > > > From: Joseph Orr <joseph....@tamu.edu <mailto:joseph....@tamu.edu>> > Date: Wednesday, April 24, 2019 at 10:51 AM > To: "Harms, Michael" <mha...@wustl.edu <mailto:mha...@wustl.edu>> > Cc: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] "activation" tables for reporting pscalar results > > > > Well I am planning on doing that, but that doesn't necessarily help with > automated meta-analytic tools like neurosynth that mine for tables. > > -- > > Joseph M. Orr, Ph.D. > > Assistant Professor > > Department of Psychological and Brain Sciences > > Texas A&M Institute for Neuroscience > > Texas A&M University > > College Station, TX > > > > > > On Wed, Apr 24, 2019 at 10:36 AM Harms, Michael <mha...@wustl.edu > <mailto:mha...@wustl.edu>> wrote: > > > > Why not simply report the parcel name and its values? And consider putting > the scene on BALSA, so that others can easily access the data. > > > > Cheers, > > -MH > > > > -- > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Associate Professor of Psychiatry > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > <mailto:mha...@wustl.edu> > > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Joseph Orr > <joseph....@tamu.edu <mailto:joseph....@tamu.edu>> > Date: Wednesday, April 24, 2019 at 10:06 AM > To: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: [HCP-Users] "activation" tables for reporting pscalar results > > > > I am trying to determine the best approach for producing tables of pscalar > results. I haven't seen any papers reporting pscalar results that have > tables, but I anticipate reviewers wanting to see these, and tables are > critical for meta-analyses. Since there aren't peaks, I was thinking of > calculating the center of mass after converting the significant parcels to a > volume. Has anyone done this already for the Multi-Modal Parcellation? Or is > there a reason that I'm not thinking of that doing this is not ideal or even > not valid? > > > > Thanks, > > Joe > > -- > > Joseph M. 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