I uploaded a dynamic MRI with multiple frames in one series. How do I separate these out (by trigger time?) so as to only segment on one individual frame?
You can load 4D volumes as either multivolume nodes or volume sequence nodes - you can set how it is loaded by default in application settings / DICOM section. You can also choose how a particular sequence is loaded if you open Advanced section in DICOM browser and click Examine then select one from the listed loadables.
Probably volume sequence is somewhat more convenient to use, as it automatically separates out a volume. You can choose which one, by using the play/pause/prev/next buttons that appear on the toolbar. You can do further processing, such as create a 4D segmentation sequence (I can give you more instructions, if needed), compute displacement fields (to propagate segmentation from one frame to all the others fully automatically; or compute landmark point positions defined in one frame in all the other frames) by using Segment registration module.
Multi-volumes have some nice time series plotting capabilities and you can enable separating out a single frame by using Multi-volume explorer module.
Thank you, that helped!
A post was split to a new topic: How can I create a 4D segmentation sequence?
Can you please give more detailed instructions for doing that?
I have 4D volume, and I want to first rigid register the volume to atlas, and the perform skull stripping using a brain mask (from the segment editor, I am doing the following
- Operation: Fill outside
- Input Volume: data
- Output Volume: “New Masked Brain”)
Now, the slicer can do this for just one of the volumes, but I want it to do this for all volumes in my multivolume data
first, the rigid registration must be done to make sure that the atlas and the brain are in the same orientation, otherwise this method will not work)
so can you give me more detailed instructions on how I can apply this manually