help > Spatial Registration Working for Subset of Channels Only
Nov 22, 2019  07:11 AM | Dylan Mann-Krzisnik - McGill University
Spatial Registration Working for Subset of Channels Only
Hello,

We are doing some pilot tests with a NIRx - NIRScout system. After converting NIRx native files into SPM-fNIRS compatible files, I have attempted to complete Spatial Registration in SPM-fNIRS UI by providing a "optode_positions_MNI.txt" file as well as a "ch_config.txt" file, along with a "NIRS.mat" file, according to the User Guide.

Oddly, the Spatial Registration seems to work for a subset of channels only. Meaning, out of the 13 channels formed by my 4 detectors / 8 sources montage, only 4 channels appear in the viewer window. I've attached a snapshot of the viewer window to illustrate what I'm referring to.

I've tried doing the same thing with the sample data, and Spatial Registration seems to work just fine. I figured it must be something with the coordinates I am inputting, or the format of the files holding the coordinates' information. I've copied the contents of the "optode_positions_MNI.txt" and "ch_config.txt" files below for reference.

The optodes and channels montage was created via the NIRSite software which generates coordinates based on the ICBM152 template within MNI space. I've noticed that the coordinates reported in NIRSite report to positions on the scalp of the template, whereas coordinates from the sample SPM-fNRIS data report to positions on the cortical surface. Maybe this mismatch is relevant.

Thank you, hopefully I have made my inquiry clear enough.

Dylan MK

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optode_positions_MNI.txt:

Optode (MNI),X,Y,Z
S1,-79.2,13.8,-18.2
D1,-84.1,-13.8,24.8
S2,-84.1,-46.4,-12.9
D2,-70.6,-78.6,25.7
S3,-56.1,-100.3,-0.8
D3,-28,-114.5,-33.4
S4,-38.8,-105,37
D4,-0,-119.5,14.2
S5,-84.8,-16.2,-16.3
S6,-82.5,-47.3,27.8
S7,-73.9,-75.6,-7.5
S8,-30.2,-116,6.8


ch_config.txt:

Ch, Source, Detector
1, 1, 1
2, 2, 1
3, 2, 2
4, 3, 1      > works
5, 3, 2
6, 3, 3
7, 4, 2
8, 4, 3
9, 5, 3     > works
10, 5, 4
11, 6, 4   > works
12, 7, 4   > works
13, 8, 4