How to increase the segmentation resolution?

Support
1

Hi everybody,

How can I increase the resolution of the segmentation as the default one uses large size of voxels (cubes)?

Is this called oversampling? how to do it without changing the volume as I need to calculate the volume afterwards?

Thanks,

2

These instructions should help: Segment editor — 3D Slicer documentation

3

Thank you so much for your reply, buddy, I really appreciate it!

If I want to segment a pericardial fat layer and then calculate the volume in cm3, will any of the mentioned 2 methods that you have provided me with, change the actual volume even slightly?

4

Usually volume changes due to smoothing and resampling are usually below 1%. You can get the segment volume from Segment Statistics module.

5

I suggest that you would want the volume of the segmented anatomy to change (slightly), because you want it to become more accurate!

On the other hand, you would want to ensure that the scaling wasn’t perturbed: for instance, if you halved the voxel size in each of the three dimensions, then you would want 8 of the new voxels to have the same volume as 1 original voxel. (Of course, any functionality in Slicer should respect this.)
And you would want to avoid excessive smoothing if your object of interest contains small features that should be retained, rather than smeared away. That is more of a judgement for you to make.

If you are concerned about this, then you can perform your own check by comparing the volume you got originally with the volume obtained from a refined/smoothed segmentation (or a series of progressively refined/smoothed segmentations).

—DIV

1 Like
6

Thank you so much guys, I really appreciate your help. That worked!

But I have another problem with the software on a different computer, when It comes to the step of data loading, it shows me this message.

“Error occurred while loading the selected files. Click ‘Show details’ button and check the application log for more information.” when I click “show details” button, It gives me this “sample 3/SER00007/IMG00001.dcm - load failed”

7

Please check if you can find any error or warning messages in the application log (menu: Help / Report a bug) and if you see any then copy it here. Make sure you load DICOM data with DICOM module (to load DICOM data, do not use the menu: File → Add data).