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Visualising FIRST vertex analysis results with FSLeyes 3D mode

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    Authored by Paul McCarthy
    1. Open FSLeyes, and open a 3D view

    2. Load these files, and ensure they are ordered like this in the overlay list::

      • Vertex analysis P value image (e.g. *_rand_clustere_corrp_fstat1.nii.gz)
      • Binary mask of the structure (*_mni_mask.nii.gz)
      • MNI152 template,
    3. Click the chainlink button next to the MNI152 to unlink it, as 3D clipping planes are linked across overlays by default, and you will probably only want to clip the MNI152.

    4. Set the display properties on each image - when working on one image, it is best to hide the other images (click the eye buttons next to their file names):

      • Interpolation -> spline
      • Number of samples -> more samples gives higher quality display
      • Blending -> lower gives a sharper display
      • Set the colour map then adjust the brighntness and contrast until you are happy
    5. Select the MNI152, and add one or more clip planes as needed to cut out the parts you want to hide.

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    Edited
    snippetfile1.txt 28 B
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