Get header info - kschan0214/sepia GitHub Wiki

Sepia requires users to supply an image header file in MAT format containing some specific acquisition information for QSM processing. You can use the utility function provided called 'Get header info' in the 'Utility' tab of the GUI to generate this header file. If you prefer directory input in Sepia, please make sure its name contains the string 'header' (e.g. 'sepia_header.mat') and put it in the same directory alongside with your other input data.

Tip: If you use MRIConvert to convert DICOM images to NIfTI format, a text file will also be generated alongside with the NIfTI data. This text file contains some basic header information including the echo times. When you use the 'Get sepia header' utility function, you can load this text file as the 'TE file' so that the correct echo time information can be extracted and stored in the MAT-file header.

(20180613 update) You can now also select multiple json files to extract the echo time information.