Operating system: windows 10
Slicer version:4.10 .0
Expected behavior:when I convert T1 series of MR in dicom format to nii format (including image and DicomRTst),Segmentation module can help me ,but when I convert DCE-MRI series ,this module can not export a nii format image,just can save as nrrd image with MRMLMultiVolume node type.
Actual behavior:
You can install Sequences extension and then load the multivolume nrrd file as “Volume sequence” (choose that in Desciption column in “Add data” dialog). If you use Sequences then you can save individual volumes in all the usual file formats, including nifti (nii).
I am very sorry that my reply is late, and thank you very much for your help!
According to your method, I have formatted my DCE sequence, but there are several patients’ DCE sequences (nrrd format，MultiVolume of Node Type) in the entire data set. After importing with the volume sequence type, use the Segmentation module to export the labelmap. The 3d slicer software is not responding(the mouse arrow is always in a circle), but most of the other patients’ DCEs only took about 5 seconds to complete the labelmap generation. What do you think of this question? Is there a problem with the original data set itself? Or do you have other ways to export the image and mask (labelmap) patient files in the nii format with a ratio of 1:1? thank you very much!
Do you have a problem with saving segmentations, labelmaps exported from segmentations, or MR volume sequence frames?
1、Does the segmentation in your response refer to the file displayed as segment in the Node Type? When I import the MR dicom image of a certain sequence and the corresponding RTst file into the 3d slicer through the dcm button, when saving, the dialog box has two file types of volume and segment, and the volume file is the MR sequence image, segment is generated by RTst file. Since I convert the format myself to extract features with pyradiomics, the image of nii format with node type is volume and the mask of nii format with node type of labelmapvolume can be run on pyradiomics code, so I have not turned and use the .seg (segmentation) type file, and I don’t know the difference between this segment and volume, labelmapvolume type files…
2、Regarding the MR sequence volume frames you said (if I understand correctly), I import the DCE-MRI dicom image into the 3d slicer (including RTst) and save it as a multivolume (node type) file in nrrd format, then use the data button to import The converted nrrd file (volume sequence selected) can complete this step, but after this step select the segmentation module and then export labelmap, this step, the software is not responding.
How do you try to extract the labelmap (which module do you use, where do you click,…)?
Segmentation module.
The use of this module is in accordance with the steps of the following post
Convert DICOM-RTSTRUCT format to Nifti format
Can you try to wait a couple of hours to see if the operation just takes too long time or crashes? Could you upload the application log of the session where the crash/hang occurred to dropbox/onedrive/gdrive and post the link here?