Lesion Review

If you have FLAIR images as well as T1-weighted images, the Brain Atrophy tool allows you to mark hyperintense lesions for a separate assessment of lesion volume and a more accurate assessment of atrophy. The lesion outlines are output to an ROI file.

If there are clear errors in the lesion outlining, there are several ways to try to make improvements:

When you want to manually edit the ROIs, instead of taking the lesion markers and propagating them to lesion outlines, the tool can use already-outlined lesions and use them as provided. To do this, take the following steps for every time-point:
  1. Load the registered FLAIR image into Jim's display and open the ROI Toolkit.
  2. Load the lesion outline ROIs produced by the Brain Atrophy tool. The lesion ROI file will have the suffix '_Lesions.roi' appended to the name of the registered FLAIR image.
  3. Make any changes to the ROIs that you think necessary.
  4. Save the ROIs not to the original file name, but the roi file name corresponding to the registered FLAIR image, overwriting the existing file.
When you have modified the lesion ROIs at all time-points, re-run the Brain Atrophy analysis from Stage 2 (Classification). Instead of propagating lesions from the Marker ROIs you provided before, the lesion outlines will be read from the files you just modified and saved, and will not be propagated further.

Note: at Stage 2, when the ROI file corresponding to the registered FLAIR images is read, any Marker ROIs it contains will be propagated to surround lesions, while any other types of ROI it contains will be used to outline lesions unchanged. So, if you wish to manually outline the ROIs rather than having the Brain Atrophy tool outline them, you just need to create an ROI file withe lesion outlines, rather than lesion markers.

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