Forum

Notifications
Clear all

digpts.txt file  

Page 1 / 2

Jordan Borrell
Posts: 8
Topic starter
(@jordanborrell)
Active Member
Joined: 3 months ago

Hey Team,

Can someone post how to create/export the digpts.txt file (as well as all the information needed in the file) that is needed to import HbO/HbR data for AtlasViewer? It isn't clear how this file is created, or where to obtain all the digit points that are needed, in the slides from the course.

Thanks,

Jordan

5 Replies
David Boas
Posts: 42
(@dboas)
Eminent Member
Joined: 4 months ago

Here is a sample digpts.txt file (the corresponding SD file can be found in day 7 of the 2020 fnirs course.

You will notice that the first 5 rows are the 3D digitized locations of the landmark 10-20 locations. These are required. The cz position can be approximate as atlasViewer optimizes the cz position given the other coordinates, starting with the initial position given in digpts.txt

This is the followed by the 3D digitized positions of all the sources and detectors.

This was covered in day 7 of the 2020 fnirs course.

I think this answers your question.

David

 

digpts.txt file:

nz: 104.3 -26.4 -4.1
ar: -10.9 -52.3 94.0
al: -6.7 -51.2 -85.1
cz: -13.9 108.6 1.4
iz: -101.8 -26.7 -5.1
s1: 1.9 28.0 -94.0
s2: -36.0 31.5 -93.9
s3: 10.0 76.0 -76.3
s4: -29.5 84.2 -75.9
s5: 16.4 105.7 -34.1
s6: -26.0 113.3 -36.3
s7: 17.6 103.7 37.5
s8: -29.2 109.4 34.3
s9: 2.7 67.9 78.0
s10: -32.4 76.1 70.4
s11: -1.5 17.9 92.4
s12: -39.6 24.2 86.5
s13: 70.6 26.1 -57.7
s14: 98.3 35.0 4.6
s15: 70.8 10.0 68.3
d1: -15.0 57.6 -90.3
d2: -53.1 56.9 -85.2
d3: -7.0 103.6 -59.8
d4: -50.2 99.2 -58.1
d5: -7.0 120.1 -18.0
d6: -50.8 116.5 -12.3
d7: -9.0 120.5 17.0
d8: -55.4 113.0 9.7
d9: -12.3 93.0 61.5
d10: -52.6 95.5 47.8
d11: -17.7 49.2 86.4
d12: -61.2 54.3 73.9
d13: 58.2 58.3 -58.1
d14: 91.2 31.9 -31.2
d15: 92.2 33.9 34.3
d16: 56.7 52.3 64.3
d17: 11.0 17.7 -89.5
d18: -27.7 34.4 -87.6
d19: 8.2 79.8 -66.8
d20: -22.8 82.0 -71.7
d21: 11.7 105.4 -26.9
d22: -30.3 110.3 -28.0
d23: 17.2 105.1 25.5
d24: -36.0 106.9 25.8
d25: 5.1 74.6 68.0
d26: -29.1 82.9 62.2
d27: -0.5 28.7 86.9
d28: -39.2 34.4 81.8
d29: 76.1 26.7 -49.2
d30: 92.7 35.9 -5.2
d31: 74.3 21.3 56.2


Reply
Jordan Borrell
Posts: 8
Topic starter
(@jordanborrell)
Active Member
Joined: 3 months ago

Hey David (and anyone else reading this),

Thank you for providing this sample file.  Are the 3D digitized locations consistent between subjects?  I have a cap with only 8 sources and 8 detectors, so way less than your file.  The sources/detectors follow the 10-20 landmarks but definitely fills space in between (focusing on motor-sensor area).  How do I create a digpts.txt file specific to my source/detector locations?  Or, do I just use the digpts.txt file you've provided as a universal basis then create my probe.SD file?  Will my probe.SD file correspond to the digpts.txt file you've provided?  I am able to get the MNI coordinates from my probe design from AtlasViewer, which I believe are correct but I'm still learning the MNI space.  I guess I'm confused on how the digit space and the MNI space correlate and transforms from one space to the next.  It looks like there's a separate software to create the digpts.txt which isn't open sourced.  Do I need to purchase this software in order to create the digpts.txt file, especially if a new, unique digpits.txt file is needed for each subject?  There's a lot to unload here, so I appreciate any and all help/direction with this.  I appreciate your time with this.

Best Wishes,

Jordan

Reply
David Boas
Posts: 42
(@dboas)
Eminent Member
Joined: 4 months ago

The 3D digitized points come from your 3D digitizer that you use to identify the 3D locations of the optodes on your subject. You also need to digitize the landmark positions on your subject so that the registration between your subject 3D coordinates and the atlas (and MNI space) can be calculated by AtlasViewer.

From your questions it sounds like you do not have a 3D digitizer. If you do not have a 3D digitizer, then none of this discussion is relevant to you.

I went back to your original question at the top of this thread and now realize I probably made assumptions about what you were asking. I thought you were asking about how to make a digpts file. But instead it sounds like you are just asking how to view your Homer3 output in Atlasviewer. Is that true?

Reply
Jordan Borrell
Posts: 8
Topic starter
(@jordanborrell)
Active Member
Joined: 3 months ago

That's correct, I do not have a 3D digitizer.  As for my original question, I was asking both: 1) I am trying to view my data in AtlasViewer and was having some difficulty, and 2) I wasn't sure how the digpts.txt file was used during that process (i.e., how is the digpts.txt file different from the created probe.SD file).  At this point, I have figured out how to display my data in AtlasViewer.  The issue there was the structure of the folders (group level, subject level, etc.), so the first issue appears to be resolved, as I am able to display my data onto the cortex under my probes. 

I'm still unsure about the second issue.  What is the difference between the digpts.txt file and the probe.SD file?  Mainly, if I've created a probe myself, it appears that I don't need a digpts.txt file.  Is that correct?  However, AtlasViewer fill pull in the digpts.txt file if it's provided, and it appears that a probe.SD file will be created automatically.  Can you explain that process in more detail?

Reply
Page 1 / 2
Share: