Re: [HCP-Users] Resting fMRI Cortex Vertices Indices

[Glasser, Matthew]

The CIFTI indices and the vertex indices do not necessarily match, as some medial wall vertices are excluded (and they are not all clustered in one place numerically).  Both the CIFTI indices and the vertex indices do match across subjects though (CIFTI with CIFTI, vertex with vertex).   Peace, Matt. From: Chao Liu <chao....@brunel.ac.uk> Date: Tuesday, June 2, 2015 at 1:07 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org Users" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Resting fMRI Cortex Vertices Indices 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 <glass...@wusm.wustl.edu> 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" <hay...@uw.edu> Date: Sunday, May 31, 2015 at 4:12 PM To: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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:hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew <glass...@wusm.wustl.edu> Sent: Sunday, May 31, 2015 11:51:41 AM To: Chao Liu; hcp-users@humanconnectome.org 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 <chao....@brunel.ac.uk> Date: Sunday, May 31, 2015 at 1:46 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 HCP-Users@humanconnectome.org 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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