Hi Francois,
I created some additional FreeSurfer surface and label files for some other ROI sets and tried to load them into BSt. I have to first load the left and right pial surfaces (lh.pial and rh.pial), then for each hemisphere load the atlases (lh.atlasname.annot). Some of these need to be renamed since they come in as lh.xxx and rh.xxx, in whichi case I rename to just xxx on each side. The next step is then to merge the two sides. However, after doing one subject successfully, I ran into problems with two other subjects. I can load the surface, display it, and load an atlas, but then the option to rename it is gone from the menu, along with several other choices. I have never seen this problem before.
I just upgraded this morning, wonder if the latest version has a bug? Of if it is my files, how can I track it down?
Thanks,
-Jeff
Hi Jeff,
The atlases that are generated by default by FreeSurfer 5.3 are considered as read only, you are not allowed to modify them. This includes the following: Desikan-Killiany, Destrieux, Mindboggle, Brodmann, Brodmann-thresholded.
If you want to modify those atlases, including renaming them, you need first to create a copy of them.
Those atlases should all be loaded automatically using the menu “Import anatomy folder”, with the option “FreeSurfer folder” selected.
This is all described in the FreeSurfer tutorial: http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
What are those additional files you create? How did you generate them? How are they named? What is the name of the final atlas in Brainstorm?
Francois
Francois,
I have no trouble with FreeSurfer atlases such as Destriuex or Des-Kil. My new problem is with the atlases we generate in-house. You helped me work out a method for using them way back when, and that method has worked fine until now, for FSrf atlases or any other ones I tried. The last time I successfully loaded these in-house atlases was perhaps last Fall, but have not had occasion to do so again until now. Of course, I am several versions of Brainstorm beyond the one I used then.
These atlases are generated using FreeSurfer tools, and I do not know whether we hace changed the version of FreeSurfer we are using. That is all done by our fMRI researchers. I can check it to it if you think that may be a problem.
As an example, let me use the Yeo atlas. After running recon-all we get the lh.pial and rh.pial surfaces, and the l/rh.aparc.annot files. Our internal pipeline additionally produces the l/rh.Yeo.annot files. Here is my procedure in detail:
load surface lh.pial
load surface rh.pial
display lh.pial
load lh.aparc.annot: this is titled Destrieux (or Des-Kil, doesn’t matter for my example)
load lh.Yeo.annot: this has the title lh.Yeo
rename lh.Yeo to just Yeo (otherwise it does not match rh side when go to merge the two pial surfaces)
unload lh.pial display
display rh.pial
load rh.aparc.annot: as for lh, this shows title as Destrieux
load rh.Yeo: this show as rh.Yeo on list of atlases
rename rh.Yeo to just Yeo
unload rh.pial display
merge lh.pial and rh.pial - this produces full brain with merged atlases Destrieux and Yeo
Like I said, this is the procedure you and I worked out two years ago and has worked fine until now. Now when I go to rename the atlas to remove the hl. or rh., I do not get the rename option even showing up.
Please try to get back to me today as this is in my critical path now. When I get to my work site I can create some screen shots to send. Thanks,
-Jeff
Hi Jeff,
I tested exactly what you describe and get the renaming options for the lh.Yeo atlas.
I can rename lh.Yeo and rh.Yeo to Yeo, so they can be merged together when merging the hemispheres.
Please make sure you are working with today’s version of Brainstorm.
If you loaded successively multiple atlases, the selected index in the drop-down list of atlases might not be updated correctly. Try to change to Destrieux, then back to lh.Yeo, and you should get the menu Atlas > Rename.
If you cannot get it to work, please send me a screen capture.
Francois
Francois,
it is all working fine now, not sure why, maybe user confusion 
-Jeff