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Hi sychoi,
That slicing does look interesting, but how do you get the whole view back? Oh, it looks like re-pressing x,y, &/or z enough times afterwards brings the view back, ok.
But I’ll have to see if that’s sufficiently useful, since moving a gyrus slightly aside as one could do with fingers or probe would seem to be more visually (& pseudo-tactilely) informative, but I’ll give the slicing a try. Thanks!
I did suspect there may not be any such tool to ‘move’ a gyrus to open a sulcus some, though I think you do have some deformation routines that could maybe be extended toward that purpose?
sychoi, thanks!
You wrote, “The surfaces we generate do not include subcortical nor extratentorial structures.”
Ok, I suspected as much.
And then gave instructions for how to do so which look doable just fine, thank you!
I’ve seen the answer as to how to save views, and it looks like exactly what I was looking for!
And removing the slices from the surface viewer by hitting ctrl+v or cmd+v is a much faster alternative to what I was doing, which was you other suggestion (@ Surface Display Sidebar, check off Show Slices). Thank you for the short-cut!
And “view your surface as a solid color” works perfectly, to allow me exercising trying to discern surface features! Wonderful! Thank you!
And I am enjoying using your interface, made all the more possible by all the answers to my questions that I’m getting! Thank you all so much! I know you all must be otherwise very busy, but these answers are very helpful and much appreciated!
Aha! Trying to save the .xml file in BrainSuite installation directory is exactly what I have been doing! It never occurred to me that I wasn’t supposed to, though it makes perfect sense that it could often/always be a no-no! Thank you so much!
Yes, just a new color scheme. Problem is I don’t see my saved description file anywhere. I first just saved a named file, and after nothing showed up, made sure to add .xml after the file name (I’d first presumed that the extent would be auto-added), but still can’t find the file(s) I’ve been trying to save anywhere. Is there any other button I should click in the label toolbox?
Oh, and I’ve tried to look for any file with today’s date, no luck.
Ok, I selected ‘View’, ‘Delineation Tool Sidebar’, selected ‘L.Insula (wm)’ at ‘description’, & changed its color as it showed in the Sidebar color selector box (but the color did not change on the brain itself).
Then I clicked ‘Save Desc.’, & entered a new filename.
Then I looked in ‘File’, ‘Open’, ‘Label Volume’, but did not find the file I thought I had created in the C:\Program Files\BrainSuite18a\svreg\BCI-DNI_brain_atlas folder. Then I closed BS, & looked directly in the above folder, and it wasn’t there. Reopened BS, looked in ‘Open’, ‘Label Volume’, & only found the main brain label file, not the one I tried to create.
Not sure what I’m doing wrong.
Thank you Anand, I’ll give it a try! And if I change some, could I cause an xml file with those changes to be saved, so I could easily alternate between different coloration schemes?
Thank you Anand, what I’d like to be able to do would be either:
1. set up BrainSuite in some way so that when I activate it, a pre-set bunch of atlas files would automatically come up at the same time, &/or,
2. know how to save ‘something’ (a ‘volume’, a ‘surface’? an atlas?) that contains all of a set of desired atlas files with a unique name, which could be simply selected as a named item from one of the BS menus to bring all of those files up (and have multiple different such named setups).I did try to load a whole directory with some of the atlas file into BS by dragging the directory itself, which didn’t work, but I can select all those files in a directory together and then drag them together, and that works.
I hope to be able to be able to select from within BS, by user specified names, different presentations of different atlases, such that one named selection might show both hemispheres, another show just one hemisphere, another with different than originally colored regions, or non-differently colored for self-test of recognition, and if interior sub-cortical structures are available, another show that one, at user selection from within BS.
I could set up different directories with different sets of files to manually drag together, which is doable but not wonderful, but I don’t know how to ‘reset’ or ‘unload’ existing ones to allow to load other different ones.
Thank you again for your reply.
oh, very sorry again! I hadn’t followed all your instructions. :( Now I do see the whole cerebrum surface! Thank you!
1. But I don’t see the cerebellum nor brainstem, and suspect inner structures are not yet showing either. How do I make them show?
2. And now most importantly, how do I save what I’ve just done, so I can add to it as I progress toward viewing what I’m considering a ‘brain atlas’ to be? The ‘Save Volume’ show 5 options, which one(s) do I need to use?
3. And can I save different views/models, so I can easily retrieve different sets of structures?
4. And is it possible to make the black slicing planes go away, or are they a necessary part of what shows the names of structures on double-click a feature?
5. And then (sorry to ask this!), how to view the un-colorized view of whole brain, so I can at some point eventually test myself to identify structures?Again, I’m sorry I didn’t follow your instructions!
Sychoi, sorry, sometimes I neglect to give useful/necessary information: I’m on a computer with Windows 8.1, and both before and after your helpful reply I did find the files you mentioned, and after your explanation dragged & dropped a number of them into BS.
1. What I found were slices, and a 3D view of those slices.
2. What I was hoping to find was something like the 3D colorized model on http://brainsuite.org/svreg_atlas_description/ .
3. And then be able to rotate that model to different views of the surfaces.
4. And then be able to modify the degree of opaqueness/transparency of surface and interior structures, in order to see structures in relation to other structures.
5. And then be able to save various views/models.And it looks to me from the descriptions on the above web page that you have segmented a nice, very large number of gyri, structures, and suci! Thank you for your work!
Does it seem that I can do the above as I’d like to do with BS, or have I misunderstood its intention/capabilities?
Hi Sychoi, and thanks! But so far I haven’t been able to see and manipulate 3-D surfaces and volumes, like the picture at part of the main page of your website, ‘Cortical Surface Extraction’, etc; have I misunderstood what BS can show & do? I had thought the Brain Atlas would show 3-D views of outside & medial surfaces and segmented interior structures, with ability to move the views to see nearby structures, and change visibility of same to see proximity relationships. (ps, I don’t mean to appear to ‘slam’ BS, it’s my fault if I’ve misunderstood what it’s supposed to do.)
