Nicola, It is possible to generate a grid on a spherical surface like Alex Cohen did in this paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705206/ … and then fold those coordinates back up into midthickness configuration. The 164k_fs_LR vertex-wise correspondence is as good as can be expected, given anatomical variability across subjects. Just having trouble understanding how you are using x,y,z coords with the myelin scalars. Donna > On Mar 29, 2017, at 12:22 PM, Timothy Coalson <[email protected]> wrote: > > If by 2D images you mean pixel-based (like .png), then the spatial > relationships can't be preserved very well. In order to make flatmaps with > moderate distortion, we have to add cuts to the cortical surface, which > leaves connected parts of cortex separated by many blank pixels. Our flat > surfaces are intended for visualization, and we do not use them for > processing. > > I would suggest doing as much of the spatial processing as you can with > wb_command - we have smoothing, gradient, dilation, and a few other things - > if you want it identical across subjects, rather than based on the cortical > distances in each subject, you can use a group average surface along with the > corresponding vertex area metric files - this is because group average > surfaces have much less folding than individual subjects, and as such, > geodesic distances along the cortical surfaces are much shorter than they > should be. > > As your earlier emails implied use of matlab, you should note that you can > load the gifti surface files into matlab, which contain vertex neighbor > information, by using the gifti toolbox > (https://www.artefact.tk/software/matlab/gifti/). The easiest way to get > vertex correspondence to the data in matlab is currently to use wb_command > -cifti-separate to convert the surface data to gifti metric (.func.gii) > files, and then load them instead. > > Tim > > > On Wed, Mar 29, 2017 at 9:24 AM, Nicola Toschi <[email protected]> wrote: > Hi, > > I'd like to arrive at a set of 2D images (e.g. 'unraveled' myelin maps > obtained by cutting and stretching out the sphere), with anatomical > correspondence across subjects, which can be used as inputs to external > proprietary algorithms (e.g. classification), so I'm pretty sure I'll need to > step out of the Workbench. > > Thanks! > > Nicola > > > > On 03/29/2017 04:18 PM, Glasser, Matthew wrote: >> What operations beyond smoothing do you need? There is wb_command >> -cifti-smoothing. >> >> Peace, >> >> Matt. >> >> From: Nicola Toschi <[email protected]> >> Date: Wednesday, March 29, 2017 at 9:09 AM >> To: Matt Glasser <[email protected]>, "[email protected]" >> <[email protected]> >> Subject: Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere >> >> Hi Matt, >> >> thank you for your quick answer! That makes sense. >> >> I would like to do some spatial operations on the sphere that exploit >> spatial neighborhood information (e.g. even simple smoothing or filtering on >> the 2D surface), and have these operations be consistent across subjects. >> >> What would be the best way to go about this do you think? Incorporate the >> exact vertex locations for each subject anyway, or ignore them and (somehow) >> just use the fact that vertex n has the same neuroanatomical meaning in >> every subject? >> >> Thanks again, >> >> Nicola >> >> On 03/29/2017 04:02 PM, Glasser, Matthew wrote: >>> We don¹t recommend using the ft_ tools with MRI data. Instead use >>> ciftiopen/ciftisave/ >>> ciftisavereset: >>> >>> >>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ >>> item 2B >>> >>> As for your other question, the vertex indices have neuroanatomical >>> correspondence across subjects, but that often does not equate to having >>> the same 3D coordinates (as volumetric registration is not able to align >>> cortical areas across subjects). >>> >>> Peace, >>> >>> Matt. >>> >>> On 3/29/17, 8:41 AM, >>> "hcp-users-bounces@ >>> humanconnectome.org on behalf of >>> Nicola Toschi" >>> <hcp-users-bounces@ >>> humanconnectome.org on behalf of >>> [email protected]> >>> wrote: >>> >>> >>>> Dear List, >>>> >>>> I am trying to do some postprocessing on myelin and thickness maps (164k >>>> versions) contained in the MNINonLinear Directory of the Structural >>>> dataset (e.g. ${subject}.corrThickness_ >>>> MSMAll.164k_fs_LR.dscalar.nii and >>>> ${subject}.MyelinMap_BC_ >>>> MSMAll.164k_fs_LR.dscalar.nii) >>>> . >>>> >>>> I thought these data would all be in the same atlas space across >>>> subjects, hence I was expecting to find the same vertex coordinates for >>>> all subjects. Instead, when reading the data into matlab ( >>>> 'ft_cifti_read' and gifti') every subject seems to have their own >>>> distinct vertex locations. Also, the spherical gifti surfaces appear to >>>> be sampled at different coordinates across subjects. >>>> >>>> Can I assume that, nonetheless, anatomical correspondence is preserved >>>> across subjects? Could I, for example, take the vertex locations from >>>> ${subject}.R.sphere.164k_fs_ >>>> LR.surf.gii, associate the scalar values in >>>> ${subject}.MyelinMap_BC_ >>>> MSMAll.164k_fs_LR.dscalar.nii to each vertex, >>>> interpolate on the sphere and assume that I can superimpose the results >>>> of this procedure across subjects? >>>> >>>> Thanks very much in advance! >>>> >>>> Nicola >>>> >>>> >>>> ______________________________ >>>> _________________ >>>> HCP-Users mailing list >>>> >>>> [email protected]http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> ______________________________ >>> __ >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. 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