Hi all! I'm working on a project involving source localisation, and I'm trying to avoid having to design my own atlases. I was wondering if anyone had any insight to help me with the following:
I have tried to load in these atlases, but I stumble at the first block. I have my
T1 MRI at 38 weeks. After I compute MNI normalisation and then try to upload the various atlases. I had the best luck with the first one (Schuh 2018), and after uploading the structures in mean/ga_38, I cannot get any type of alignment, using either the embedded transformations or no. I then tried using the included T1 in the source, and that doesn't work either. I'm imagining I've missed something obvious, so any advice would be appreciated.
I tried the other two atlases, and I couldn't figure out how to import them at all. Help?
I have also tried to use that atlas and I have not managed to import the tissues or anything, I even tried to do it from scratch with the CAT12 and the average MRI t1, but it gives a lousy quality, (C-),I guess then that the files are wrong
I spent some time investigating this and found a solution for the Schuh atlas.
To use it, you will have to import the T1 as normal. Then, use the import MRI function to import structures.nii.gz. Be sure that when you are importing structures, you have selected "Volume Atlas (Subject Space)" as otherwise it will not import correctly. I didn't see this option described anywhere in the documentation, so I imagine it could be made clearer in the tutorials. Segment using CAT12 in the "run" section to include cortical thickness, etc.
A few other things to note would be that the dHCP processing pipelines make extensive use of Developing Brain Region Annotation With Expectation-Maximization (Draw-EM) within MIRTK v2.0. I don't know if Brainstorm has any plans to improve functionality between these at any point, but it might be worth investigating or seeing if these pipelines could be integrated into Brainstorm.
I continued to work with this atlas, however CAT12 doesn't produce a suitable extraction of the surface. Although it provides a A-B in the extraction, it produces a model with a diagonal longitudinal fissure and therefore cannot be appropriately analysed with source analysis. It is also unsuccessful with BrainSuite, but I am less familiar with Brainsuite and may have missed something. Any tips? @tmedani
I've also looked specifically at the CAT12 and SPM12 databases, but have not had luck yet.
CAT12 is simply not designed to work with data from neonates. The youngest age you can process is around 1–2 years old. It is almost impossible to develop morphometric tools that can cover the age range from neonates to adults with reasonable quality. This is why only a few customised tools exist that focus on neonates only.
