Fast manual lesion segmentation in ITKsnap

When finished, save the newly drawn image with "Segmentation" - "Save Segmentation Image".
This is a video-tutorial showing the basics of drawing brain lesions in ITKsnap. The interpolate tool allows the user to draw the lesion every few slices, and then interpolate the drawings to create a full lesion. Obviously, this method serves well if the lesion forms just one 3D shape. If the lesion for your patient forms more than one 3D shape, you can interpolate one part, and draw the other slice by slice. You can also label the different parts with different values, and interpolate each of them separately (i.e., first Label 1, then Label 2). In this case you would need to merge the labels in another software (thresholdImage in ANTs, or some c3d command).

[@ramanareddy1000]

Thank you, this video helped me to sort out several issues.

[@shengchuangfeng227]

Helpful! Thank you!

[@wangderek9688]

Thank you for this very helpful video. I am wondering if I can know more about the reference of the paper (cranium 2013?) you mentioned in the video which provides the rule to identify lesions.

[@lesymap1691]

Should be:
Crinion, J., Holland, A.L., Copland, D.A., Thompson, C.K., Hillis, A.E. (2013). Neuroimaging in aphasia treatment research: quantifying brain lesions after stroke.. NEUROIMAGE, 73 208-214. doi:10.1016/j.neuroimage.2012.07.044

[@eshachoudhary99]

Hi! Thank you for such a great video. This is really helpful. I had a question after we are done with the segmentation how do we mark it as done.

[@lesymap1691]

You just save the segmentation file with "Segmentation" -> "Save". There is no other marking as done, the segmentation lives in the memory of the computer/itksnap until you save it out as a file.

[@abhijeet6989]

Thank you very much sir for your valuable guidance.
How to convert segmentation image into tiff format?

[@lesymap1691]

Not sure, but there is a function in the menu somewhere to output multiple slides as common bitmaps. Don't know if tiff is a format you can choose there.

[@muhammedyusufkurt7404]

Thanks for this useful video. I have a question. How can we measure the volume of the area to the segment? After loading three dimensions, I find a result from the segmentation and volume option, but it is not very accurate.

[@lesymap1691]

If you go to Segmentation -> Volumes and Statistics in ITKsnap, you should find the volume you need. The volume is the product of voxel size by the number of voxels. You can also calculate it in other programs outside ITKsnap.

[@muhammedyusufkurt7404]

When we do, we find the value containing "e". I was stuck here. I found the solution. We multiply by 10 as the number of digits after "e". The next value we found is the volume in mm3.

[@iramshahzadi357]

very helpful video. I wonder if I could get the link to download paper mentioned in this video (5:02) about rules of drawing lesion. anyone?

[@lesymap1691]

Link: www.ncbi.nlm.nih.gov/pmc/articles/PMC3534842/
We are also working on a book that will contain segmentation rules, but it will not be out before next year.

[@iramshahzadi357]

Thanks a lot!

[@lucasfernando4655]

Hello, can you please tell me what is your professional occupation or what academic degree you have? I'm a biomedical engineer and I want to work with medical segmentation of the brain. Any tips on how to enter in the field? Thanks!

[@lesymap1691]

I am not a biomedical engineer but have a phd in neuroscience. I cannot give you a sound advice. It will likely depend on your geographical area, whether there is a university nearby, whether there is a group that does segmentations, etc. I can tell you that these things are not difficult after all. It is all a matter of numbers, all images are numbers, whether you take the picture with a phone or an mri machine.

[@lucasfernando4655]

@@lesymap1691 Thank you!

[@Sapos93]

Bro is labelling Sylvian fissure and calling it a lesion xd

[@aanchalchoudhary9934]

sir can you tell me which Statistics method is used in lesymap and please add you email