AtlasViewer: 'Warning: No cortical anatomical labels provided for this anatomy'

[Franziska Klein]

Hey everyone,

I am trying to coregister fNIRS and fMRI data and everything works fine until I want to project the probe to the cortex (AtlasViewer v2.8, p2.1).

I conducted the following steps:

1. creating a probe ('Make Probe') and put my digitzer data into digpts.txt file

2. segmentation of subject specific MRI via freesurfer (recon-all)

3. put *.SD and digpts.text into 'mri' folder of the freesurfer output

4. being in that 'mri' folder path: start AtlasViewer from the command window (Matlab 2016a) and click File -> Import MRI Anatomy; AtlasViewer takes all the files needed and I click SUBMIT

5. Click Tools -> Reference Points -> Find Nz, Iz etc and find the corresponding fiducials

6. Clcik Tools -> Reference Points -> Calculate

I am not sure about the next step, however, when I am not doing it I cannot click on the 'Register Probe to Surface' button and it works when I use the Colin anatomy instead of the subject specific anatomy:

6. Click Tools -> Register Atlas to Dig Points

7. Click 'Register Probe to Surface' Button

And when I  finally 8: click on Tools -> Project Probe to Cortex -> Project a window pops up with the message: 'Warning: No cortical anatomical labels provided for this anatomy'. 

When comparing my anatomical folder with the Colin anatomical folder I realized that I don't have the labelssurf.mat file which is also the reason for the warning message from the AtlasViewerGUI.m 

I tried to find a function within the AtlasViewerGUI folder in which this labelssurf.mat is generated but I was not succesful. I am not an expert for this huge amount of output files I get from freesurfer but since there is a folder called 'labels' I thought this is somehow used in AtlasViewer to create such *.mat file. 

Am I doing something wrong here and if yes could someone please advise me here?

Thanks,

Franziska

[Franziska Klein]

Is there no one who could help? Or maybe some ideas who I could ask directly for help?

Thanks,
Franzi

[Boas, David]

If you can share a link to a folder with all of the files that you run AtlasViewer in, then we can try to recreate the issue you are having to identify what you are doing wrong.

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[Franziska Klein]

Thank you very much for your response.

Here the link with an untouched (in terms of AtlasViewer output) data folder of one of the subjects: https://drive.google.com/drive/folders/11D_RfbJQLzTleRf9N2hwKBZUOsM7Zi5_?usp=sharing

This is the freesurfer output folder. In the main folder (s28) you can find the digpts.txt for that particular subject and within the mri subfolder I've put the Probe.SD file.

Thank you so much for looking at this problem.

Kind regards,

Franziska

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[shann...@gmail.com]

Hi Franziska,

Did you find a solution for your issue? Are you able to project the probe coordinate onto your individual MRI?

Shannon