Two Questions: I have dicom files from MRI which have all necessary metadata, however, only some of the files are consecutive, while others are skipped in between (i.e Dicom 001, Dicom 002, Dicom 007, etc.) The ImagePositionPatient says the spacing is .3mm, and from the 43 files I have, the total…

Hi - For number question 1, you can turn on geometry regularization and it should automatically handle the missing slices: [image] For question 2 I can’t think of an easy way to do this. A little python script would be the easiest. Or do it manually to create new segments per slice (maybe usin…

[image] epdawson: For the length of a volume that was created via segmentation, it is possible to get the volume of each slice individually after the model is created? I am interested in the areas of all the segmented slices, but have only been able to do this by loading in a single slice at a t…

Hi Steve and Andras, Thanks for the responses. When turning on geometry regularization, the slices are now placed in the correct location. However, when segmenting, I am unable to add masking to any slices that are past the max z location of the previously truncated series. The truncated z locati…

Probably default segmentation labelmap geometry is not computed optimally for non-linearly transformed images. You can adjust it by clicking the button next to the master volume selector (see this post for some instructions). Or, you can harden the regularization transform using Transforms module.

Dicom File Loading Spacing

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Davide_Punzo (Davide Punzo) November 13, 2023, 8:31am 6

NOTE: Support for regularization transform hardening in DICOM Scalar plugin has been added. See link.

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Dicom File Loading Spacing

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