Dear community,
I am trying to work with sLORETA to obtain source estimates of EEG with volume model. The issue seems to be that when I use PTE I only see 157 scouts. When I go back to the brain model I see only 157 scouts. Didn't it import 170 scouts. Is that a bug? Or am I doing something wrong?
I imported from AAL3 option of the atlas if I don't recall wrongly. Or I could have done it with AAL3 atlas from their website. Either way there is only one choice because the other doesn't brign labels.
Thank you for all the help in advance.
None of the above. The confusion may come from the term atlas, as it can mean volume parcellation (labels for voxels in the MRI) or a collection of Scouts (defined in the volume grid).
Consider that in the case of AAL3 volume parcellation, there are labels that correspond to voxels in the cerebellum.
Thus, when you create the AAL3 volume atlas (set of scouts) with the AAL3 volume parcellation, as shown in [1], volume scouts will created for places where the volume grid and the volume parcellation labels overlap. As such, if the volume grid was defined only in the cortex volume [2], the scouts for the cerebellum will not be created, there are not vertices there, as consequence there will be less Scouts in the volume atlas than labels in the volume parcellation
Example: in the individual anatomy below, the AAL3 volume parcellation had 164 labels (top). When imported as volume scouts for the volume grid (bottom left) defined in the cortex volume, results in (bottom right) 127 scouts. Note that there are not scouts in the cerebellum.
I know the terms aren't accurate. Sorry for that. But the atlas scouts are, let's say 170 ad then I have 157 but I do have scouts from the cerebellum. Just not all the cerebellum parcellation areas appear. Is that normal?
Unfortunately, I do not understand your question. Where are the 170 Scouts? where are the 157 Scouts? If possible add screenshots to have better context regarding your question.
the 170 scouts do never exist. I only have 157 ( when I import them for the parcellation) The 170 they are gone the labels of the atlas. AAL3. I need these labels and coordinates MNI for each.
I'm afraid I do not understand the context of the question.
- Please be explicit, which meaning of the word atlas are you using, so we can be in the same channel
What do you mean?
This is my guess on what is going on.
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The AAL3 defines 170 anatomical parcellations.
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But there is not certainty that all of them are going to be used. When importing an MNI-parcellation as indicated in this tutorial (https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#MNI_parcellations), a label is assigned to each voxel of the subject anatomy based on its coordinates in the MNI space. There is not a correspondence of one-to-one, so it can end with less than 170 unique labels.
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When using an anatomical parcellation to generate a volume scout atlas, the scouts are defined in the source grid not in the volume space, so again, there is not certainty that all the labels in the imported anatomical parcellation are going to be used. Because, for each vertex in the source grid, a label is obtained as the label for the closest voxel in the subject anatomy. There is not a correspondence of one-to-one, so it can end with less than than the unique labels in the imported anatomical parcellation.
If this does not describe your situation, please share relevant and detailed information.
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I think it is 3 point discussed above. Thank you for the comments. I think then there is no possibility that I can create a volume scout atlas with 170 labels or scouts.
