Hi,
I am a beginner user of Brainstorm. I am working with both the EEG and fMRI signal of some subjects, my main goal is to extract information about some scouts time series in order to compute connectivity. I am able to perform this task with default atlases; however, my main concern regards the use of a custom atlas, provided by a third person.
Up to now i have a .nii file of the atlas, which is a 3D matrix of dimensions 181x217x181, single type (when loaded into Matlab). This cube contains the numbered labels of 220 ROIs, cerebellum ROIs excluded.
I also have a region_Description 220x1 cell array (containing the labels name) and a regionDescriptions_number double array, 220x2, containing the labels number (the same number appeating in the volumetric matrix of the atlas) and the labels of the main brain regions the ROIs correspond to (e.g. first 5 labels are Precentral_L_p1/2/3/4/5, all contained in the major brain region Precentral_L, numbered 1 in the second column of the regionDescriptions_number).
I'm struggling with the task of importing this atlas and parcellation (Note: I may be using the words atlas and parcellation in an incorrect way).
Let's take, for example, the case of the data contained in the introduction tutorial. After importing subject's anatomical data (with Import anatomy folder --> selecting anatomy folder) and importing some EEG data (let's not consider that EEG data belongs to other subjects, is just for practicing), how do I compute the source estimation and extract scouts from my custom atlas?
The .nii file should be in the MNI coordinates: plotting its volume and comparing it to the volumes of other atlases (e.g. desikan.Cube), returns very similar results, all oriented in the same way.
Thanks for your attention,
Zanchi
HI @Zanchi
Your post contains multiple topics and questions.
First of all, I recommend you follow the introduction tutorials to get familiar with the software and the database; after that, I'm sure you will have some answers to your questions:
Get Started: https://neuroimage.usc.edu/brainstorm/Tutorials#Get_started
If you have you have your atlas as a nifti file (.nii) you can import it to Brainstorm as an MRI file.
You can also check with your third party provided if its format is compatible with the files and atlas available in Brainstrom. Or you can import it and co-register it to the default models.
To compute the source, you need to understand how to process to EEG data and then how to compute the forward and inverse solution as explained in the introduction tutorial and particularly at the tuto 20 to 23
Importing a .nii file as MNI anatomical parcellation:
https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#MNI_parcellations
Then this anatomical parcellation can be used to create volumetric Scouts:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases
As indicated by @tmedani, please follow the Get started tutorials to get familiar with Brainstorm and its jargon.