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Couple of atlasviewer questions - "finding" reference points and installing atlas

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Meredith Pecukonis
Posts: 16
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(@meredith)
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Joined: 2 years ago

Hello! I have two questions about atlasviewer.

 

1. When I import subject specific MRI anatomy and am prompted to select reference points (Cz, Iz, Nz, LPA RPA), should I just select these points by "eyeballing" and estimating where these points are on the head? Any tips on how to improve the accuracy of selecting these points?

2. I have a segmented atlas file available in -.nii format that I'd like to import into atlasviewer to identify which specific regions my probe is covering. When I use the dropdown "install atlas" function in the atlasviewer GUI, it states that the folder where my -.nii file is located is not a valid directory. Is there any way to get the -.nii file in the appropriate format so that I can import it into atlasviewer? 

 

Thanks for your help!

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David Boas
Posts: 238
(@dboas)
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Joined: 2 years ago

I gather you already looked at the lecture here

https://openfnirs.org/training/homer-premium/training-courses/20201019-member/fnirs-course-day-6-october-27/

I just looked at the lecture and it doesn't explicitly state the format needed for importing MRI... strange.

That lecture maybe does provide pointers on choosing the ref points though. Also, a series of papers by Ippeita Dan speaks to this point. Here are some of the paper citations:

1. Tsuzuki D, Jurcak V, Singh AK, Okamoto M, Watanabe E, Dan I. Virtual spatial registration of stand-alone fNIRS data to MNI space. NeuroImage. 2007;34(4). PMID: 17207638
 
1. Jurcak V, Tsuzuki D, Dan I. 10/20, 10/10, and 10/5 systems revisited: Their validity as relative head-surface-based positioning systems. NeuroImage. 2007;34(4). PMID: 17207640
 

 

There are specific details on how to import MRIs on the wiki here

https://github.com/BUNPC/AtlasViewer/wiki/Importing-Subject-Specific-Anatomy

 

 

 

 

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Meredith Pecukonis
(@meredith)
Joined: 2 years ago

Active Member
Posts: 16

@dboas thanks so much! 

 

For those using MRIs from the neurodevelopmental database, here's some info that I received from John Richards that might be helpful in regards to selecting reference points:

 

When you download MRI zip folder, inside the sources --> electrodes folder, you'll find a series of excel sheets/tab files that have coordinates for anatomical reference points. More info about those excel sheets can be found in the document that is called "KeyToElectrodesAtlasOther" (also in downloaded zip folder). In the fiducial file, 2 = Nz, 3 = Iz, 4 = LPA, 5 = RPA, 13 = Cz. Note that in the fiducial files, the units are meters. The first one is the anterior commissure/AC marker and the rest are offset from the AC. To determine the xyz voxel number, add each fiducial to the AC, multiply by 1000, round. This will give you xyz voxel coordinates, which you can use when selecting reference points in atlasviewer.

 

 

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YiShu Li
(@lys)
Joined: 9 months ago

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Posts: 6

@meredith excuse me, have you solved the 'install atlas' problem? i want to use icbm 152 as the atlas but idk how to import the atlas

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