Automatic c-MRI heart segmentation


I have cardiac short axis scans which I would like to segment at specific phases of the cardiac cycle : at peak-systole and at peak-diatole.

So far, I manually detected the relevant slices and then copied the IMA file to a new folder [one for the systole and one for the diastole] , and then used the DICOM patcher for volumetric segmentation.

*Is there an automatic feature to extract the slices?
*How can I group all the relevant slices to one nrrd flie?
*Sometimes I get the following error : Unexpected error after executing the patch command: ‘ForceSamePatientNameIdInEachDirectory’ object has no attribute ‘patientName’
I tried to change the metadata accordingly - didn’t work.

Thank you for your help,


Latest Slicer version should be able to automatically load 4D cardiac MRI sequence as a volume sequence. If it does not seem to work then you can share an anonymized data set (upload somewhere and post the link here) and we can investigate.

Thank you for the quick reply.
I downloaded and installed the latest version. The 4D cardiac MRI sequence was indeed loaded automatically as a volume sequence, and I was able to segment the whole heart at once. However, I wasn’t able to nevigate through time periods. [I was able to segment only the specific loaded time frame].
Up till now I have uploaded the data without using the DICOM utility and used the scroll bar to choose the desired time period.
I am newbie to this module and I would appriciate your assistance in the matter.

The entire data is available at the following link: