I did read up on FrSrf file formats last night (especially annot and surf), and what you tell me here helps clarify some things. I am now thinking that my best bet may be to try to obtain the original Yeo atlas, which hopefully I can then use to create matching surface+annot combinations for my individual subjects. I am told we have matching surface+annot combinations already, but I have not found them yet.
To clarify, should I get the “magic” number error when I try to import one of our local annot files? Or do I always have to first import a matching surface file first?
We were able to find the appropriate surf and annot files and import first the left and then right pial surfaces followed by the Yeo annotations. I can merge the left and right pials into a cortex, but cannot quite figure out how to combine the two annotations into a single Atlas. Please advise me on that part.
Import lh.pial, load lh..annot from the scout tab.
Import rh.pial, load rh..annot from the scout tab.
Select imorted lh+rh surfaces, right-click > Merge.
This will combine the atlases of each hemisphere.
OK, that makes sense.
I discovered during this process that the “Import Freesurfer folder” does a little cleanup on the pial surfaces, resulting in a slightly reduced number of vertices. THis was throwing me off when I initially tried to import the Yeo atlases since they no longer matched. Thus I believe that if I want to use the local Yeo atlases I need to go back and manually import the MRIs and pial surfaces again, if I want to have the two built-in FS atlases as well as the Yeo atlas for my subjects. Does this sound right?
Yes, if you want to add custom atlases, you cannot use the menu “Import Freesurfer folder”, you have to import everything manually.
How do you get the Yeo atlas for the individual subjects?
A research assistant in our lab did it about 2 years ago using Freesurfer tools. I think you know the process: align each individual to the generic Yeo atlas on the sphere, then map to the individual cortex inflated to a sphere, then map back to the folder 3D cortex, then to the voxels if you need that as well. I hope to learn how to do this soon as I will have new subjects I will need to perform it on.
Another question comes to mind. Now that I have manually imported the Yeo atlas as well as Destrieux, Desikan-Killiany, Brodmann, and two others we have here, I want to subparcellate to use as a scout. But I have to do that for each individual, and they will not mecessarily match. What I really probably need to do is subparcellate in the general Yeo or other atlas space. So I presume I have to do that first in Freesurfer, using the FS parcellation tools, then create an individual subparcellation “labeling” before importing each individual into BST.
FreeSurfer 5.3 does not generate individual versions of this Yeo atlas, so it’s not available on any other brain.
You can ask them if they are planning to integrate this atlas in the default FreeSurfer segmentation at some point.
Now I try to apply Schafer or Yeo's atlases onto my lh.pial as you describe here and I got message saying number of vertices are not matching! So question here is, you know we can define the number of vertices when we upload the freesurfer anatomy folder to brainstorm, would this make any effect on the number of vertices of already segmented surface files or does it only related to source reconstruction related definitions, I mean saying to Brainstorm how many of those vertices I want a dipole to be fitted? Sorry for asking this questions I really do not know how those things works in general really.
So do you think would it help us if I would identify the number of vertices let say as 10242 when I upload a freesurfer segmentation folder to brainstorm, so it changes the number of vertices on segmented file hence later on I can use fsaverage5 atlas? If not is there any other way of downsampling the number of vertices of our surface files to the one required for the atlas we would like to use? I would really appreciate if you could help me with that please.
Ps. I would have tried myself and see obviously but somehow I cannot upload freesurfer files to brainstorm, alhough I did before, which gives me very weird error which I do not understand the reason.
Thank you,
Now I try to apply Schafer or Yeo's atlases onto my lh.pial as you describe here and I got message saying number of vertices are not matching!
How are you proceeding?
we can define the number of vertices when we upload the freesurfer anatomy folder to brainstorm, would this make any effect on the number of vertices of already segmented surface files or does it only related to source reconstruction related definitions, I mean saying to Brainstorm how many of those vertices I want a dipole to be fitted?
Brainstorm imports the high-resolution surfaces generated by FreeSurfer, loads the atlases on top of them, and then downsamples the surfaces with Matlab's reducepatch function to get a reasonable number of dipoles for source reconstruction. The import procedure is detailed here, and these are the instructions you should refer to to load any additional atlas: https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy
If not is there any other way of downsampling the number of vertices of our surface files to the one required for the atlas we would like to use? I would really appreciate if you could help me with that please.
You won't be able to do anything like this. You have to start with full resolution surfaces, import all the atlases, and then downsample.
Apparently this application works with the annot/label files produced by Freesurfer during MR segmentation however I cannot make it work with any other atlas file outside the freesurfer segmentation folder. I attached the error message that I get if I try to upload that or any other Yeo atlas (the number of the mismatched vertices change depends on the atlas that I am trying to upload of course).
So my confusion, even though we didn't indicate the number of vertices during segmentation in freesurfer how my segmentation ended up with 134570 vertices hence it does not match the vertices of the atlas that I am trying to upload. And if I use CAT12 to run all the segmentation from the very begining, and choose 15000 vertices for the segmentation, so how come later on this segmentation could work with any Yeo atlas, whose vertices are different from 15000 vertices already but it fits somehow, but I cannot make it work manually. So does this mean, during segmentation there is a separage lh.pial files are produced for each of the default atlases anyways so they match with the annot file somehow, and since I am lacking this in my freesurfer segmentation hence I cannot upload any Yeo or Schafer atlas at all? I would really appreciate if you could give a bit more details about that please indeed. Because if I already have segmentations files are ready for all the subjects obtained with freesurfer and you know it takes ages to complete for a whole set of participants, and it would be really helpful if I can find a way to upload Yeo or Schafer atlas onto those segmentations.
No, indeed.
You need to find a way to project your atlases on the individual brains first, and then import them into Brainstorm. I don't know how to do that, but there are probably ways with FreeSurfer.
I've just been told by Chris (Markiewicz) freesurfer's mri_surf2surf function might be doing it but haven't had a chance to have a look. Once I get more info and practices I will report here but for now several links about the function itself is here
