nube; how2: access/use brain atlas

Forums Forums Installation and Setup nube; how2: access/use brain atlas

This topic contains 6 replies, has 2 voices, and was last updated by  DanM 3 months, 1 week ago.

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  • #1247

    DanM
    Participant

    Hello, I just downloaded BrainSuite to use the included brain atlas; I’m not a medical professional, just thought to try to use BrainSuite to aide in trying to learn brain anatomy, and I don’t see how to access & use the atlas. Can anyone help?
    I see the page, ‘using Atlases with other softwares’, and see that there are two atlases present in the svregmanifest.xml file, and that they are supposed to appear in the SVReg dialog box, but I don’t see how that will let me view either of the atlas.
    What do I do to see the atlas?
    thank you in advance.
    Dan

  • #1248

    sychoi
    Participant

    Hi Dan, our atlases will be found with your installation files. for example

    for windows:
    C:\Program Files\BrainSuite18a\svreg

    for mac
    /Applications/BrainSuite18a/svreg

    you will see a directory for the BCI-DNI_brain atlas and BrainSuiteAtlas1. I recommend the BCI-DNI_brain atlas.

    drag and drop files ending in:
    .bfc.nii.gz (or BCI-DNI_brain.nii.gz for inclusion of skull and scalp)
    .left.mid.cortex.dfs
    .right.mid.cortex.dfs
    .all.dfc (right and left will only load one at a time)
    and under File–>open–>label volume
    select the “BCI-DNI_brain.label.nii.gz” file

    To give you a few tips:
    you can learn about navigation controls here: http://brainsuite.org/interface/
    you can click anywhere on the volume slices or double click anywhere on the surface and the name of the region will appear on the bottom of the interface. There’s also some fun things you can do for visualization by opening up the mask toolbox.
    You can see the names and description of the sulcal curves (.dfc files) by opening up the sulcal toolbox

    click around, experiment and have fun. Let us know if you have any other questions.

  • #1249

    DanM
    Participant

    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.)

  • #1250

    DanM
    Participant

    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?

    • This reply was modified 3 months, 2 weeks ago by  DanM.
  • #1252

    DanM
    Participant

    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!

    • This reply was modified 3 months, 2 weeks ago by  DanM.
  • #1291

    sychoi
    Participant

    The surfaces we generate do not include subcortical nor extratentorial structures.
    You can generate surfaces from any mask or label.

    If you have the svreg.label.nii.gz file loaded, open up the tools–> mask tool–> label mask tool
    then click “update list”
    you can then select any ROI (subcortical structures are in the 600s) and then click “make surfaces for each label”
    These surfaces can be saved using the surface display toolbox (hit “s” and it will appear or Surface->Show Surface Display Properties Toolbox)

    Your question on saving views was answered here: http://forums.brainsuite.org/forums/topic/bci-dni_brain_atlas-how2-save-retrieve-different-views/

    you can remove the slices from the surface viewer by hitting ctrl+v or cmd+v
    you can also unclick “slow slices” option in the surface display toolbox. Specific orientations can also optionally be turned off.

    You can view your surface as a solid color by going to the surface display toolbox.
    select your surface then select “solid color”
    unclick that and your colorized surfaces will be reappear

    Good luck. Glad you’re enjoying our interface

  • #1297

    DanM
    Participant

    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!

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