Tracked-Ultrasound with external image data adjustments [Matlab]

I have a Tracked-Ultrasound system that combines tracking information and image data. Within this set-up I would like to export the imaging data to Matlab, make adjustments (segmentation), and import again. As the image must be altered in Matlab individually, 3D reconstruction won’t work for that latter.

Therefore, I record an sequence with the tracking information (.seq.mha) and imaging data (.seq.nrrd) that can be exported. Now I have a problem to import the files in Slicer again. The sequence metafiles are seen as individuals and can not be combined. I get either a moving thing with a still or the imaging acquisition on the same spot.

Could anyone help?