I am trying to segment CT image. The data format is .nrrd and I can import it to Slicer successfully. I checked the import data and the voxel value is HU, which is from about -1000 to 1000.
However, when I use the Threshold feature in Segment Editor, the threshold range is limited to [0, 99], and I can not change it. I also tried to choose different Automatic Threshold (auto->maximum, minimum->auto, as lower, as upper), but it does not make any change.
I am a new user to Slicer. Am I missing something? Any suggestions are greatly appreciated. Thank you very much!
Does it work correctly in latest Stable Release or in recent Preview Release? If not, could you please send the application log (menu: Help / Report a bug)?
Hi,
I have two Slicer Version in my work PC. But both have problem. In Version 4.10.2 I can not croped the Volume. In Version 4.11. I can select the Threshold Range but the Apply function is not work and I dont get 3D Modell. My data have 10GB.
I’ve tested loading of a 10GB volume then segmenting in Segment editor using Threshold effect then create 3D model by enabling “Show 3D”. I’ve found a bug that caused Slicer to exit during model generation, but I’ve fixed it now, so Slicer Preview Release that you download tomorrow or later (revision 28581 or later) should work well.
Task manager shows that you are running out of memory. The error message tells the same. Configure 50-100GB more virtual memory or crop and/or downsanple the image before starting segmentation.
The flag allows you to indicate for yourself that you a segment is correct and complete. It is essential when you have hundreds of segments. See details here: New feature: Search and filter in segments table
Hi,
3D Slicer is not work for DICOM Data.
I have the hard disk rate system expanded to 3TB. I can only open a finished 3D reconstruction, but I can not load a DICOM. What could be the problem?
PC:
intel Core i7-9700 CPU 3,00GHz
64GB
64Bit
Windows 10 Version 1803
D-Laufwerk: 2,72TB
C-Laufwerk : 238GB
Hi All,
I seem to be running into the same issue with my threshold range. It is coming in at -2038.26 to 11956.00 which is way above HU units range of -1000 to 1000. Am I missing something or is this an error?
The displayed threshold range is the volume’s intensity range. If it has these large numbers then it means that your volume has such large numbers in it. Even a single outlier single voxel value will alter the min/max value. You can get voxel position of these outliers using numpy:
a = array('MRHead')
import numpy as np
indices = np.where(a>200)
for i in range(len(indices[0])):
print(f"voxel {i+1}: index = {indices[2][i]} {indices[1][i]} {indices[0][i]}, value = {a[indices[0][i],indices[1][i],indices[2][i]]}")
