There should be no need to split the original DICOM series in Matlab. Install sequences module, import the DICOM files into the DICOM database using DICOM module, then load it as a volume sequence (if it is loaded by default as a MultiVolume then go to menu: Edit / Application settings / DICOM / Preferred multi-volume import format -> volume sequence).
You can segment the CT at one timepoint and warp the segmentation to all other timepoints using Sequence Registration module as described in this topic: Load multiple cardiac phases for segmentation/virtual reality