Number of time series when downsampling to atlas does not coincide with number of ROIs in atlas

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1

I have a .nii file with an atlas that has 214 ROIs, each one coded by intensity level. When I open it with the MATLAB function niftiread I see that it has 215 unique values (0 to 214).

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I was able to load it into my cortex file after segmentation of the subject's MRI, and it looks like this:

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imagen1106×840 211 KB

However, when I downsample to this atlas after source reconstruction, I get 216 time series. How can this be the case? (The example corresponds to one trial with 2500 temporal samples).

imagen

Thanks in advance.

2

The step you need to check is the import of your parcellation.
Check the Atlas field in the cortex surface:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#On_the_hard_drive

Note that we don't recommend using this process "Downsample to atlas".
I added a new warning in this process:
image

3

When I'm loading the atlas it says it's creating 214 scouts:

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But in the end it creates 216, I don't really understand? The atlas field in the cortex surface has 216 regions.

4

Note that using a volume atlas from a .nii volume to create surface atlases is not an accurate procedure.
If you need to use an volume anatomical atlas with volume ROIs, it could be a better option to use volume source models and volume scouts.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource

If you want to keep working in the same direction, please share the example file you are trying to load here: upload it (zipped) somewhere and post the download link here.

5

For reproducing the behavior you describe, I would also need:

  • the cortex surface on which you are trying to load the atlas an (the .mat file from the Brainstorm database)
  • the reference MRI of the subject (the first one in the anatomy folder)

Please zip these two files together with the .nii atlas and share it with us.