Exporting transformed data

Support
,
1

Operating system: Windows
Slicer version:4.6.2
Expected behavior: Transform location of an ROI (label) and export the transformed data as a DICOM
Actual behavior: Exported ROI is at the same location.

Hello,
I am trying to create ROI on multiple different phases of MRI that are taken at the same time. Since images are not in the same orientation, I need to move the original ROI to align it to subsequent phases. Here is the procedure that I follow.
Create ROI (label-1) via Editor module on the first phase, save DICOM using subject hierarchy. Go to next MRI phase and align the ROI(label-1) to it using transform module. Harden the transform in in data. Resample image using BRAINS module with following specifications:
Image to wrap : label-1
Reference Image: label-1
Output: create new label map as…
Next I export the new output image (which is the transformed label) as a DICOM using subject hierarchy.
Loading both DICOMs to image J, I see the mask at the same location, meaning original ROI got exported not the transformed version.
PS: I am pretty new to Slicer, there might even be an easier way to moving a label and saving it as a new mask.
I also have feel like there could be a problem with the software that I use to lead the DICOMs (Image J), because when I load them to Slicer, the transformation has been applied.
Sincerely
Faraz

2

Hi Faraz,

A few suggestions:

  • Please use the latest nightly, there have been many improvements
  • Use Segment Editor module instead of Editor, it has more advanced functionality, and more robust data handling

What DICOM modality are you exporting to? This is very important to know so that we know which exporter you use exactly.

3

Thank you for your response Csaba,
I use subject hierarchy, I drag the label under the corresponding study and use the default setting to Export DICOM by right clicking on the label.
I will try the nightly version. Meanwhile do you know of any other way that I could do this: Creating a label and exporting it as a mask (DICOM), then moving the label and exporting another mask.
Best
Faraz

4

Using Resample scalar/vector… module (instead of BRAINS) will allow you to select the transform and apply it to the desired output volume.