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:
- Provide more Marker ROIs. If there are whole lesions or parts of lesions being missed, you
can place more Markers on the lesions to give greater coverage. This may be especially useful
if there are diffuse or confleunt lesions.
- Change the setting of the
slider. Increasing the threshold will reduce the size of the lesions, and
vice versa. When you have found the optimal setting for your MRI scanner and pulse sequence,
you should not make further adjustments.
- Manually edit the ROIs that outline the lesions and re-do the analysis using these corrected
outlines.
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:
- Load the registered FLAIR image into Jim's display and open the
ROI Toolkit.
- 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.
- Make any changes to the ROIs that you think necessary.
- 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.