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help > Surface and Nodes rotated 90 deg?
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Feb 7, 2017 10:02 PM | Daniel Stolzberg - University of Western Ontario
Surface and Nodes rotated 90 deg?
Hello,
I have just started using BrainNet and I made custom Edge, Node, and NV surface files. I can view these files in BrainNet, however, the surface representation of the brain is rotated (looks approximately by 90 deg) relative to the Nodes. I'm assuming I am doing something wrong writing the NV or the Node file coordinates, but I can't figure out what that might be.
To make the NV surface file, I used the vertices and faces obtained from a GIFTI surface file.
To make the Nodes file, I first read in my atlas regions using [Y,XYZ] =spm_read_vols(AtlasVolume), found the centroids of my regions of interest, and then used the values in XYZ as the coordinates for the nodes file.
Both the nodes and nv surface file seem to display nicely in BrainNet viewer, but they are rotated relative to one another. I've attached an image showing this.
Does anyone have any suggestions?
Many thanks,
Dan
I have just started using BrainNet and I made custom Edge, Node, and NV surface files. I can view these files in BrainNet, however, the surface representation of the brain is rotated (looks approximately by 90 deg) relative to the Nodes. I'm assuming I am doing something wrong writing the NV or the Node file coordinates, but I can't figure out what that might be.
To make the NV surface file, I used the vertices and faces obtained from a GIFTI surface file.
To make the Nodes file, I first read in my atlas regions using [Y,XYZ] =spm_read_vols(AtlasVolume), found the centroids of my regions of interest, and then used the values in XYZ as the coordinates for the nodes file.
Both the nodes and nv surface file seem to display nicely in BrainNet viewer, but they are rotated relative to one another. I've attached an image showing this.
Does anyone have any suggestions?
Many thanks,
Dan
Feb 7, 2017 10:02 PM | Daniel Stolzberg - University of Western Ontario
RE: Surface and Nodes rotated 90 deg?
Never mind! My dimensions were wrong on my Nodes file.
Feb 9, 2017 11:02 AM | Mingrui Xia
RE: Surface and Nodes rotated 90 deg?
Hi,
I guess the issue is caused by the coordinates of the surface vertices. I'm not sure which direction is right in your case. Please use the button "Data Cursor" to locate the exact coordinate on the surface, and modify the vertices by exchanging and taking the opposite numbers.
Best,
Mingrui
I guess the issue is caused by the coordinates of the surface vertices. I'm not sure which direction is right in your case. Please use the button "Data Cursor" to locate the exact coordinate on the surface, and modify the vertices by exchanging and taking the opposite numbers.
Best,
Mingrui