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]<mailto:[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]<mailto:[email protected]>>
Date: Sunday, May 31, 2015 at 4:12 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[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]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>>
on behalf of Glasser, Matthew
<[email protected]<mailto:[email protected]>>
Sent: Sunday, May 31, 2015 11:51:41 AM
To: Chao Liu;
[email protected]<mailto:[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]<mailto:[email protected]>>
Date: Sunday, May 31, 2015 at 1:46 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[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]<mailto:[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. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
[email protected]<mailto:[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. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
[email protected]<mailto:[email protected]>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
--
This message has been scanned for viruses and
dangerous content by MailScanner<http://www.mailscanner.info/>, and is
believed to be clean.
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
