Essentially, yes, but don't call a cifti index a vertex, and note that it is specifically the left cortex vertex 68. You may also want to look at the -cifti-export-dense-mapping command:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-export-dense-mapping There is also code available for C++ and matlab that will read cifti files, including parsing the xml, and give access to these translations directly, the two github links here: http://www.nitrc.org/frs/?group_id=454 Tim On Tue, Jun 2, 2015 at 6:07 AM, Chao Liu <[email protected]> wrote: > Hi Matt, > > Thank you very much for your explanation. > > For the first 29696 vertices (left cortex) and then 29716 vertices > (right cortex) in the rsfMRI data, are the vertices arranged according to > the order shown in the xml information?: > > <BrainModel IndexOffset="0" IndexCount="29696" > BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT" > ModelType="CIFTI_MODEL_TYPE_SURFACE" SurfaceNumberOfVertices="32492"> > <VertexIndices>0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 > 18 19 20 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 > 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 … > > > For example, suppose I identify the 21st vertex as activated in the rsfMRI > data (91282 by 1200), and since vertex 68 appears in this position in xml > file, is it right to say it is vertex 68 that is actually activated? > > Cheers, > Chao > > On 31 May 2015, at 22:17, Glasser, Matthew <[email protected]> > wrote: > > Hi David, > > How this is done is explained in the Pipelines paper in fMRISurface > pipeline’s section (page 18 last paragraph of section). Basically one uses > the individual subject subcortical segmentations and nonlinear volume > registration to map individual subject voxels onto a standard atlas set of > subcortical voxels. This process will be as good as the nonlinear > registration and subcortical segmentation (which is also true of the > surface process, its only as good as the surface registration and the > quality of the surfaces themselves). > > Peace, > > Matt. > > From: "David R. Haynor" <[email protected]> > Date: Sunday, May 31, 2015 at 4:12 PM > To: Matt Glasser <[email protected]>, "[email protected]" > <[email protected]> > Subject: Re: [HCP-Users] Resting fMRI Cortex Vertices Indices > > Hi matt, > > One other thing. I understand that if you take the grayordinate locations > of the vertices and apply the appropriate spatial transform, one gets the > vertex locations in subject space, along with labels, so you have > corresponding cortical points across subjects, with the same vertex having > the same label across subjects. > > How does this work for the subcortical voxels? If you apply the same > transform to the set of grayordinate voxel locations, you don't wind up > with a consistent set across subjects. The points in subject space won't > always be in different voxels. They can't be, because the volume of the > subcortical structures varies across subjects. Is it possible to get a set > of consistently labelled points in subcortical structures, or can this only > be done at the level of subcortical structures (20 or so, rather than 30K, > per subject)? > > -dh > ------------------------------ > *From:* [email protected] < > [email protected]> on behalf of Glasser, Matthew < > [email protected]> > *Sent:* Sunday, May 31, 2015 11:51:41 AM > *To:* Chao Liu; [email protected] > *Subject:* Re: [HCP-Users] Resting fMRI Cortex Vertices Indices > > Yes they are and they have correspondence across subjects. That is the > point of being on standard meshes and a standard atlas set of subcortical > voxels in the 2mm CIFTI grayordinates space. The reason that not all > surface vertices are included is because the medial wall is not cortical > grey matter. > > Peace, > > Matt. > > From: Chao Liu <[email protected]> > Date: Sunday, May 31, 2015 at 1:46 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Resting fMRI Cortex Vertices Indices > > Dear Experts, > > In resting state fMRI dtseries file, by using wb_command > -file-information xxx.dtseries.nii, we could see: > > CortexLeft: 29696 out of 32492 vertices > CortexRight: 29716 out of 32492 vertices > … > > And by using wb_command -nifti-information xxx.dtseries.nii -print-xml > we could see: > <BrainModel IndexOffset="0" IndexCount="29696" > BrainStructure="CIFTI_STRUCTURE_CORTEX_LEFT" > ModelType="CIFTI_MODEL_TYPE_SURFACE" SurfaceNumberOfVertices="32492"> > <VertexIndices>0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 > 18 19 20 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 > 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 … > > which tells us which 29696 vertices (CortexLeft) out of 32492 are > included. And for CortexRight, it tells which 29716 vertices out of 32492 > are included. > > My question is are all the vertices indices in CortexLeft (29696) and > CortexRight (29716) the SAME for all the subjects? > > Thank you very much for your time! > > Cheers, > Chao > > > _______________________________________________ > 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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