How can I convert 2 different echotime magnitude b0map into phasediff file?

[npdrbong]

Hello, I am very sorry for newbie question.
I am trying to unwarp fMRI file using b0map.

And I have some trouble with SIEMENS triotim data, sequence name is “*fm2d2r”.

for some subject, It include 1 magnitude map and 1 phasediff map, but in some subject, It only includes 2 magnitude map for different echotime (_e1.nii.gz, _e2.nii.gz)

And both subject has same count of dicom files, (39 dicom files for each echotime) so I wander about what’s wrong with this

I searched in neurostar about this and found this article, but It seems not perfectly match with my problem…

Field mapping ( Siemens scanners)- dcm2niix output 2 BIDS

For Siemens users who get “_Eq” images: this occurs because Siemens scanners can generate the same series (0020,0011) and instance (0020,0013) number for the same slice acquired for two echoes. In this example, where the fieldmap had 36 slices, saving the data direct from the console would store 72 DICOM files, but when the images got exported the PACS archiving thought there were duplicates and only saved 36 (in this case, 5 from one echo and 31 from another). This is not a fault of dcm2niix: …

dicom_hdr (e1/e2)TE6.50_000001.dcm | grep "0020 0011"
0020 0011        2 [2110    ] //              REL Series Number//5
$ dicom_hdr (e1/e2)TE6.50_000001.dcm" | grep "0020 0013"
0020 0013        2 [2130    ] //            REL Instance Number//26
$ dicom_hdr (e1/e2)TE8.96_000001.dcm" | grep "0020 0011"
0020 0011        2 [2110    ] //              REL Series Number//5
$ dicom_hdr (e1/e2)TE8.96_000001.dcm" | grep "0020 0013"
0020 0013        2 [2130    ] //            REL Instance Number//14

$ dicom_hdr (m/ph)TE6.50_000001.dcm" | grep "0020 0011"
0020 0011        2 [2108    ] //              REL Series Number//5
$ dicom_hdr (m/ph)TE6.50_000001.dcm" | grep "0020 0013"
0020 0013        2 [2128    ] //            REL Instance Number//35
$ dicom_hdr (m/ph)TE8.96_000001.dcm" | grep "0020 0011"
0020 0011        2 [2108    ] //              REL Series Number//6
$ dicom_hdr (m/ph)TE8.96_000001.dcm" | grep "0020 0013"
0020 0013        2 [2128    ] //            REL Instance Number//21

I have a question that if I can convert e1 and e2 files into phasediff file, or if I can get phasediff file from this dicom file. thanks a lot!

[neurolabusc]

When you acquire Siemens gradient echo fieldmaps it is critical that you reconstruct both the phase and magnitude images. This will generate two magnitude images and a phase difference image. For details, see the FSL documentation and my sample data and additional notes.

The tool fslcomplex allows you to convert complex data (real + imaginary) to phase and magnitude (aka absolute) values. However, it is impossible to derive the phase information from the magnitude data. Therefore, data where only the magnitude images were acquired are insufficient for FUGUE spatial undistortion.