Thanks @Steven . Does this mean that the scanner directly saved the phase difference image ? As I mention there were only 37 dicom files (37 slices in volume). The reason I wasn’t sure was because I could only extract TE2 from the header for each dicom file – giving the impression that these are TE2 raw phase maps as opposed to phase difference map. On the other hand, dcm2niix somehow knows what TE1 is and includes it in the json sidecar file.
@ins0mniac2 you should check your scanner console and make sure you are saving both magnitude and phase reconstructions. You can see this in your Siemens sequence PDF as Magn./Phase.
Thanks @neurolabusc . Pretty sure we are. Data sorted into folders by series look like this (sequence supposed to have 37 slices):
Folder 1 : 37 dicom files (magnitude image, checked visually) – some echo 1 , some echo 2. dcm2niix detects the issue and makes “Eq” files.
Folder 2 : 37 dicome files (phase image, checked visually, but not certain whether raw phase or phasediff). dcm2niix is happy, creates e2_ph files, json has both Echo Time 1 and Echo Time 2, although I can only see one Echo Time (TE2) in the headers on all files using dicom_hdr.
Since dcm2niix detects both the echo times for the phase image, it is clearly a phase difference image. Since you have only 37 images with the Eq, it is clear that some magnitude images from one echo overwrote some of the images from another echo. It is clear that some tool that handled these images only looked at instance number (0020,0013), mediaObjectInstanceUID (0002,0003) to detect duplicates. You want to check the provenance of these images to identify the tool and remove it. Your situation is just like Siemens series 2 and 3 from this repository. While the DICOM standard does not require unique instance numbers (hence your data is technically legal), in my experience it is the leading cause of data loss by Siemens users. I strongly urge you to contact the Siemens Research Collaboration Manager associated with your center and lobby them to resolve the problem at the source.
Thanks @neurolabusc! These are old data but the local imaging folks have been alerted. My only remaining question is – what header field is dcm2niix looking at to extract both TE from the phase difference series ?