Hello,
I’ve run into what I believe is a contradiction on the Case 4: Multiple phase encoded directions (“pepolar”) of the latest BIDS specifications.
In GE one can not only acquire b-value = 0 diffusion weighted images (1 volume - 1 b-value=0, as you can do in Siemens), but you always have to acquire DTI volumes (7 volumes - 1 b-value = 0 and 6 b-value = 1000 (or any other b-value)). So if one wants to acquire diffusion weighted images with different phase encoding direction he needs to acquire at the very least the following two series:
Series 1: DTI volume with pepolar 0.
Series 2: DTI volume with pepolar 1.
Of these, one will be AP and the other PA, satisfying the requirements to apply this fieldmap correction case 4.
As you may see, the normal consideration of these images is DTI, see that the two of them have b values=[0, 1000, 1000, 1000, 1000, 1000, 1000]. Thus, I believe their name/folder structure should be as follows: dwi/sub-01_dir-AP_dwi.nii.gz and dwi/sub-01_dir-PA_dwi.nii.gz and they should be accompanied by their corresponding bval/bvec files.
However, according to the standard, at the very least one of them should be in the fmap directory, and have the extension _epi.nii.gz .
- Are my assumptions correct until here? What should be the correct behavior?
Next the second problem comes with the usage of IntendedFor, B0FieldIdentifier and B0FieldSource with their json. Regardless of fmap vs dwi location of either of the files above. My goal is to use both images for fieldmap estimation, and also to correct the two of them.
As for my understanding, the two of them should have the same B0FieldIdentifier and B0FieldSource but if we want to be compatible with IntendedFor. The two of them should also have a IntendedFor list containing the two of them (on recursive pointing to the same file, and the other to the other file).
- Is this correct?
Thank you very much for your help.
Oscar