Dear Donna and Tim, thank you very much for your replies and insights. Yes, flatmaps is exactly what I was looking for!
For now, I was just taking the xyz positions on the sphere, converting to polar coordinates, interpolating and resampling the myelin on a regular grid along the two angular coordinates, hence resulting in a 2D image. From you explanation I understand that this would preserve topological neighborhood relationships between scalar values but not so much real (geodesic) distances, right? Thanks a lot! Nicola On 3/29/2017 9:29 PM, Dierker, Donna wrote: > 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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