wb_view example - edickie/ciftify GitHub Wiki

building a figure in wb_view

Pretty Figure

Step 1: open wb_view

When you see the splash screen click Skip, we will load the files manually..

Click on File -> Open File to open the file browser *Note: the filter (at the bottom) is set to only show you .spec files... Click on this and switch to "Any Files" Click on "null_WG33" and select all files (CRTL-A) and click "Open".

  • S900_AverageT1w_restore.nii.gz
  • S900.L.white_MSMAll.32k_fs_LR.surf.gii
  • S900.L.pial_MSMAll.32k_fs_LR.surf.gii
  • S900.L.very_inflated_MSMAll.32k_fs_LR.surf.gii
  • S900.R.pial_MSMAll.32k_fs_LR.surf.gii
  • S900.R.very_inflated_MSMAll.32k_fs_LR.surf.gii
  • S900.R.white_MSMAll.32k_fs_LR.surf.gii
  • S900.sulc_MSMAll.32k_fs_LR.dscalar.nii

Click on the "neurosynth_maps" folder and then select both files and click "Open"

  • working_memory_pFgA_z_FDR_0.01.nii.gz
  • working_memory_pFgA_z_FDR_0.01.dscalar.nii

Getting our tabs in order..

  1. Click on the first tab (1) Montage
  • at the bottom you should see the Overlay toolbox.
    • click on the top toggle under File and select the working_memory_pFgA_z_FDR_0.01.dscalar.nii
    • make sure it is checked on
    • click on the bottom toggle and select the S900.sulc_MSMAll.32k_fs_LR.dscalar.nii
    • and check it on

  1. Click on the (2) Volume tab:

    • At the bottom Overlay Toolbox - Select Layers Tab:
      • For the top layer - toggle the File to working_memory_pFgA_z_FDR_0.01.nii.gz
      • click on the wrench to the left of the filename to open up the Overlay and Map Settings
      • In Overlay and Map Settings, change the Palette (middle left toggle) to "PSYCH"
    • Click on the Vol/Surf Outline Tab:
      • Click on the outlines for the white and pial surfaces..
          • Note: the locations of the group "white and "pial" average surfaces, are they where you expected them to be??*
    • At the top of the screen in the Slice Plane section, click on the All button to show all three views..
    • Click around the image to explore it a little.. note every time you click, the Information toolbox will pop up to tell you the intensity values at the curser..
    • keep clicking around until you have chosen your favourite view of the images

  2. Close the Tabs (3) All, (4) CortexLeft and (5)CortexRight

  3. From the File menu: Click on View -> Enter Tile Tabs

  • move the (2) Volume Tab to the Left of the (1) Montage Tab by clicking and dragging

make the colour scales of the two images match

It seems like a color scale of 3 to 8 sounds reasonable let's do this for both images: Click on the wrench beside the top layer of the overlay toolbox to open the Overlay and Map Settings toolbox.

  • Turn on the threshold and change to set to 3.5
  • change the palette to "PSYCH"
  • change the palette to from "Percent" to "Fixed"
  • change the Pos Max "Fixed" value to 8.5
  • un-check "Negative" so that only Positive Values are showing

Palette Change

Now do the same for the dscalar image..

Add the RSN networks to the background of the surface view..

  • Load the Yeo 7 Network Atlas: File -> Open File (Select null_WG33/RSN-networks.32k_fs_LR.dlabel.nii)
  • Click on the (1) Montage Tab
  • In the overlay toolbox, toggle the middle overlap to *RSN-networks.32k_fs_LR.dlabel.nii" and click the checkbox to display it
  • Click on the wrench beside the RSN-Networks to open the Overlay and Map Settings toolbox
    • Note: now that we are dealing with label data..the Labels dialog is visible instead
    • change the Drawing Type to Outline Color
  • Now click on the Briefcase Icon on the top right corner to open the Features Toolbox
    • Turn all labels off by click the All: Off button
    • Under the 7 RSN Networks.. Menu check the 7Networks_6 label..

Features Toolbox

Add some labels to the figure

-In the Mode Section of the Toolbar Click the Annotate Button

  • The Annotation let's you add Text, Objects and Images directly into the scene
  • You have 4 option for how to anchor the object you would like to add
    • St: Anchor to an MNI coordinate
    • Sf: Anchor to a surface vertex
    • T: Anchor to a location within a tab
    • W: Anchor to a location within the whole window (or figure)
  • For this example let's add text (T) anchored to the window (W) After clicking on these buttons click on the location where you would like to add text and a text box should pop up.
  • Add the text "Working Memory (neurosynth.org)"

Save your figure into a scene!

  • Click on the directors slate (top right corner) to open the Scene's Dialogue
  • Click on new to create a new scene file..PUT is one directory above the source files you have loaded
  • Click Add to add you new figure to the scene file

Save everything you have done

In the file menu, click on File -> Save/Manage Files -> Save Checked Files

  • also save the changes you have made to the palette for the working memory maps..

And we are done