Hello everyone, I hope that you are doing fine in these hard times? I have a question regarding segmentation export. Is there any way to export segmentation or even whole study DICOM data without segmentation (CT or MR) as bin (binary) file that could be later on imported in Monte Carlo N Particle…

Slicer-4.11 is hugely improved compared to Slicer-4.10, including optimized memory management for segmentations. In some cases (when you have hundreds of non-overlapping segments in a segmentation) then memory usage and computation times may be decreased by a factor of 10-100x in Slicer-4.11.

I believe we have a complete set of import/export tools for EGSnrc Monte Carlo engine. I’ve found Dosxyz NRC 3D dose file reader in SlicerRT extension but did not find others. @cpinter can you give more information on this? Regardless of this, you can always export the segmentation to a labelmap vo…

Dear @lassoan , Thank you for your reply. I have installed SlicerRT but can’t find the mentioned Dosxyz extension or manuals for the rest of the applications in Radiotherapy section. Since I am no expert at python and coding, is there another approach to the problem (regarding to second part of you…

In SlicerRT we indeed support a complete DOSXYZnrc workflow. For example, this is the call from python to the ctcreate utility that saves the CT data in a format that DOSXYZ can read. You don’t need to be an expert to understand this code, as a matter of fact, I don’t consider myself a python expert…

Thank you for your reply @cpinter . Actually, I don’t know any of coding and since I am in medical filed, this whole thing is really new to me :). I’ll have to find someone who could help me with that. As I have already made the whole model (stl file), combining two persons DICOM data, and is it pos…

Reading in this file in Slicer would not be hard it seems. There are many examples for such a reader, like the one @lassoan referred to. If you check out the differences between the two file formats and modify the code according to the few differences, then it should be really easy to have a working…

I segmented neck, thorax, abdomen and pelvis from one person, but didn’t have whole head… Then, I segmented head (brain, skull, eyes) of another person. In 3d modeling software i combined these two and made one whole model of head, neck, thorax, abdomen and pelvis. Is it possible to import that whol…

I suggest against this heterogeneic approach. STL files do not explicitly contain information about the coordinate system, so depending on the method of saving the file in your chosen application, they may appear on top of each other. In either case (appear correctly vs need to manually align) you c…

That is what I thought, import it as labelmap, that shouldn’t be a problem. The exporter that you mention, is it DOSXYZ? This next steps are confusing to me and that is the main problem :confused:

The exporter I mean is for the MCNP toolkit you use and it does not exist yet, it needs to be created. The DOSXYZ exporter can be a good starting point and serve as a sample. It is a programming task to create this exporter, and it is not hard at all, just read the existing code, and change what is …

Hello guys, it’s me, again :frowning: I need help, again. So, I manage to import stl files of different organs in 3d slicer and when I try to save all of them as segmentation (.nrrd file) message pops up saying “Exception trown in event: Bad allocation” Few days ago I manage to do same but only w…

Export segmentation as bin file

Support

Topic		Replies	Views
Exporting DICOM directory after segmenting lesion Feature requests	13	1551	December 17, 2018
Save segmented images Support	4	1576	July 10, 2021
Export volume with burnt-in segmentation Support segmentation , dicom	4	1297	January 2, 2019
Export binary mask of the segmentation as jpeg/png Support	2	874	April 18, 2024
Save segmentation output as xml file or binary mask Support	4	2431	February 6, 2019

Export segmentation as bin file

Related topics