Are volumes.txt correct?

[treanus]

Thx for making available hd-glio-auto!

I observed a possible problem with the reported values in volumes.txt.

Seems like the reported volume in mm3, equals the number of voxels in the segmentation, but not the actual volume in mm3!
If voxel sizes are isotropic 1x1x1 mm these are correct.
However, when using a different resolution the output seems to be wrong.

An fslstats -V of the different segmentations shows this.

[jenspetersen]

Hi! You're actually correct, we're just counting voxels, probably because I copied that part from somewhere else where we actually resampled to 1mm isotropic. This doesn't happen here, so it's a pretty embarrassing oversight, thanks for raising the issue! There will be a new release soon, with that part fixed of course :)

[giemmecci]

Hi, thanks for sharing HD-GLIO!

I wondered if this has been fixed since I have the same issue described by @treanus.

Thanks!

[jenspetersen]

Hey @giemmecci @treanus, sorry for the delay. There is a new version that you can currently get with docker pull jenspetersen/hd-glio-auto:test. I will also move it to the default tag soon, but if you have time to test that would be great!

[giemmecci]

Thanks so much, and no problem at all!

I will test it starting in June and will let you know. Thanks!

[giemmecci]

Hi,
The issue seems to be gone with the new version: in the attached figure, the output of the previous version is on the left, and the one of the latest version is on the right; as you can see, in the new version, the total volumes are in line with ITK-snap.

I have tested it only on one case, but I will keep using the new version and monitor the output.

Thanks!

[giemmecci]

Hey @giemmecci @treanus, sorry for the delay. There is a new version that you can currently get with docker pull jenspetersen/hd-glio-auto:test. I will also move it to the default tag soon, but if you have time to test that would be great!

Hi @jenspetersen,
Has the test version been moved to the default one?

Thanks!