questions > Using dcm2niix on pepolar scans
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Mar 25, 2019  11:03 AM | Lauren Hopkins
Using dcm2niix on pepolar scans
Forgive this horribly beginner question.
I have just collected my first field maps to use for distortion correction from a GE Discovery MR750. These are 2 pepolar scans.

Does running dcm2niix on pepolar scans create field maps that can then be used in preprocessing streams such as FMRIPREP? In other words, if I run
dcm2niix -f pepolar1 /PEPOLAR1/FOLDER

is this call that needs to be done to create a field map that can be used for distortion correction? Are other flags required (I did not see any in the help) or is further processing needed after running this command?
I'm mostly asking because I'm not exactly sure what to look for to guarantee the created .json and .nii files are, in fact correct. For example, I used the above command on 2 pepolar scans and the ensuing .json files indicated the same phase encoding axis (j), which I thought would be different between the two scans. However I'm not sure if this is the right place to look.

Thanks for any help on how to deal with pepolar scans.
Mar 25, 2019  05:03 PM | Chris Rorden
RE: Using dcm2niix on pepolar scans
This depends on how your scanner was set up. As I note on the web page, GE scanners can be set up to generate different types of images from a field map. Hopefully, you can visually inspect your images to determine what type of scans were stored from the sequence.