Hi Alfonso,
Thank you for your reply. In the attached archive, the file 'run-8.json' is the one previously discussed.
I also want to ask a related question. When I tried to use the 2nd default pipeline including the fieldmap-based distortion correction, I got the following errors:
warning: unable to find EchoTime1 or EchoTime information in [. . .]\conn_project01\data\BIDS\sourcedata\sub-0001\run-6.nii
warning: unable to find PhaseEncodingDirection information in [. . . ]\conn_project01\data\BIDS\sourcedata\sub-0001\ref_run-8.nii
ERROR DESCRIPTION:
Error using conn_setup_preproc
insufficient information for vdm creation. Skipping subject 1 session 1...
The protocols are as follows:
run-6 - fieldmap amplitude (2 images in one file)
run-7 - fieldmap phase
run-8 - fMRI
Consistent with the above error message, I did not find EchoTime in run-6.json, although run-7.json has a field "EchoTime": 0.0074 (the larger of the two echo times).
Also in the file run-8.json, I did not find PhaseEncodingDirection.
I could get around this fieldmap issue by converting from DICOM to nii and json by the program MRIcroGL. It produced JSONs with all the above-mentioned fields, and I am attaching them for reference (files with long names denoting protocols).
It would be good if this could be fixed in CONN, so that there is no need to switch between programs.
Best,
Dmitry