Manual editing capabilities??

[cogito]

Hello,

I'm not certain if this is the proper forum in which to post this question, but here goes:

Does BrainVISA or its affiliated programs allow for the manual editing/deletion of skull, scalp, and flow artifact data? I'm working with FLAIR data from patients with ischemic white matter damage and semi-automated thresholding skull/scalp extraction techniques, like BET, do not work with imaging data where the white matter lesions approximate skull in terms of grey values. Also, BET truncates the range of grey values, which is a problem for subsequent analysis of white matter volumes.

What I need is a voxel-level editor that will allow me to go slice-by-slice and erase the skull and scalp. Does BrainVISA do this? If not, any other suggestions for non-commerical or reasonably priced software that may accomplish what I want?

Thanks,
Jeff

[Yann Cointepas]

Your question is in the right place because Anatomist contains a 3D voxel drawing feature that we use to correct automatic segmentation when it is necessary. This is exactly what you want to do. However, this feature has not been designed to directly modify an image but to create a graph structure containing the regions drawn. There are tools in the BrainVISA package for conversions between images (either binary images or label images) and graphs but I am not sure there is a tutorial to explain all the steps.

These steps are groupped in the BrainVISA process editors->automatic->Label volume editor. It is designed for the correction of the hemispheres and cerebellum segmentation from a T1 image but it should work with any kind image.

[cogito]

Thank you for taking the time to respond to my query, Yann.

I'm curious about graph feature. Does this yield a graph of voxel intensity values within any particular ROI? If so, then this close to the histogram segmentation technique I'm trying to use isolate ischemic white matter volumes, which will be defined by the upper tail of the range of FLAIR voxel intensity values once the skull, scalp, and other non-brain material is excluded.

Regards,
Jeff

[Jean-Francois Mangin]

The graph story is something different, just a format. You can easily get it converted
in a standard label images. The drawing tool is not completely user friendly,
but you have an online help.