AtlasViewer: Checking if individual MRI was imported correctly

[Shannon Lim]

I am a bit concerned about how my MRIs are importing. Here are the steps I have been taking that raise some concern:

1. run "setpaths"

2. run "AtlasViewerGUI"

3. load subject folder containing:

- digpts.txt

- digpts.SD

- Anatomy folder (segmented using SPM12: T1.nii, grey.nii, CSF.nii, wm.nii)

4. Register Atlas to Dig Points

5. Register Probe to Surface

6. Save Viewer State

7. Project Probe to Cortex (Curr subject channels)

8. I save these projections in Excel then close everything (including matlab)

9. Rerun steps 1-6

10. Import MRI Anatomy

11. load head (T1.nii), CSF (CSF.nii), brain (grey.nii), white matter (wm.nii)

12.  looks like AtlasViewer runs through: Noise reduction, Recaling, Rescaling, Filling gaps generating head surface from volume, Downsampling, duplicating?, Downsampling, Generating pial surface, Downsampling pial surface

13. Select basic reference points

14. Calculate EEG reference points

15. Project probe to cortex (Curr subject channels)

16. Save these projections in Excel to compare.

On multiple occasions, the projections in step 8 and 16 are exactly the same.

Are there any steps I'm missing or doing incorrectly?

Has anyone had issues with this?

Is there a way to check if individual MRIs have been imported correctly into AtlasViewer?

[Boas, David]

we have a long tutorial on how to do this at

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

 

Have you seen that page?

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[shann...@gmail.com]

Thanks David,

I was using this page for reference: https://www.nitrc.org/plugins/mwiki/index.php/homer2:Importing_Subject-Specific_Anatomy_Importing

I believe the instructions are identical.

I think I just solved my original issue... but a new issue has come up

FYI: I had previously opened AtlasViewer to the subject-specific directory that contained the digpts.txt and digpts.SD files and a folder where the subject-specific anatomy is. Even though I loaded the MRIs within that folder (step 3 and 4), for some reason originally loading the subject-specific parent folder with the anatomy in a separate folder in AtlasViewer didn't allow the anatomy to load properly. I then tried loading a subject-specific folder with all the contents not in folders in AtlasViewer and it seems like the individual MRI loaded properly.

New issue: When I "Project probe to cortex" it now says "Warning: No cortical anatomical labels provided for this anatomy." Does this mean that AtlasViewer does not have the ability to project the probe to individual MRIs?

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[Boas, David]

You mentioned this

New issue: When I "Project probe to cortex" it now says "Warning: No cortical anatomical labels provided for this anatomy." Does this mean that AtlasViewer does not have the ability to project the probe to individual MRIs?

Atlasviewer does not have the ability to provide anatomical labels for user supplied MRIs. Sorry about that. I believe this is just a warning. Does it still provide MNI coordinates? I forget. 

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On Aug 19, 2020, at 7:54 PM, shann...@gmail.com <shann...@gmail.com> wrote:



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[shann...@gmail.com]

Hi David,

I don't see any MNI coordinates provided. Is there a way to calculate these MNI probe projections from imported MRIs?

If the probe projections are not possible with imported MRIs, what is the purpose of importing MRIs? Is it for visualization purposes?

Thanks,

Shannon

[Shannon Lim]

Hi David et al.

Is someone able to answer my last questions?

"I don't see any MNI coordinates provided. Is there a way to calculate these MNI probe projections from imported MRI

If the probe projections are not possible with imported MRIs, what is the purpose of importing MRIs? Is it for visualization purposes?"

Thanks!!

[Boas, David]

The original purpose for importing MRIs was for visualization and calculating the forward problem for image reconstructions.

Absolutely, it would be nice to project MNI coordinates on imported MRIs. That code exists in the MRI community. We never had time to implement it in Homer.

Would be great if someone could help with that task!

As a start, identify the opensource code that produces the MNI transformation for subject specific MRIs.

From that point it should be more straight-forward to get it working in AtlasViewer.

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