BCI-DNI_brain_atlas: how2 differently color some gyri?

Forums Forums Installation and Setup BCI-DNI_brain_atlas: how2 differently color some gyri?

This topic contains 7 replies, has 2 voices, and was last updated by  DanM 10 months, 2 weeks ago.

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  • #1258

    DanM
    Participant

    Hello, I’d like to differently color some gyri (eg, insula, so as to be better able to see it in contrast to nearby superior temporal gyrus); how can I do that?
    (And then of course, be able to save that without losing the ability to retrieve the original colorization.)

    Thank you.

  • #1280

    Anand Joshi
    Moderator

    You can choose the colors of individual ROIs by using the label tool.
    http://brainsuite.org/delineation/roi/label-painter-tool/

    You can modify the colors, recolor and save the surfaces.
    If you want back the original color, you can click on load description, select the label description xml file in the atlas directory and then goto surface view and select color by labels.

  • #1283

    DanM
    Participant

    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?

  • #1285

    DanM
    Participant

    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.

  • #1286

    Anand Joshi
    Moderator

    You are not creating new labels, just the new color scheme, right?
    You can load the original volume, then open label. this will show labels in the original color scheme.
    to load your new colorscheme, open label toolbox, load description and load the xml file that you saved. this should show the changed colors.

  • #1287

    DanM
    Participant

    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.

    • This reply was modified 10 months, 2 weeks ago by  DanM.
  • #1294

    Anand Joshi
    Moderator

    Not sure why that would happen. Please make sure that you are saving the xml file in the directory where you have write access. Perhaps you tried to save it in a read only directory, like BrainSuite installation directory?

  • #1296

    DanM
    Participant

    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!

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