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| If you acquire complex-valued data, you should (1) split the data into magnitude and phase files (NOT real and imaginary!) | ||
| and (2) retain a copy of the bval and bvec files with the part-mag entity included (i.e., do not use the inheritance principle on these files). |
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Doesn't this conflict with below where you need to have files with both the part-mag and the part-phase
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You need them for each file for BIDS (e.g., with both part-mag and part-phase or without part at all), but you need it with part-mag for QSIPrep.
So this is BIDS-valid:
sub-01_dwi.bval
sub-01_dwi.bvec
sub-01_part-mag_dwi.nii.gz
sub-01_part-phase_dwi.nii.gz
But on the other hand you need this for QSIPrep:
sub-01_part-mag_dwi.bval
sub-01_part-mag_dwi.bvec
sub-01_part-mag_dwi.nii.gz
sub-01_part-phase_dwi.nii.gz
Note that the part-phase bval and bvec are not needed for QSIPrep.
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I'll make changes to make this clearer
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@arokem I'd love to get your thoughts on my changes before I merge. |
| The inheritance principle ensures that the bvals and bvecs without the ``part`` entity | ||
| apply to both the magnitude and phase files. | ||
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| Unfortunately, if you do this, QSIPrep will not be able to find the bvec and bval files. |
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Definitely worth documenting until we have a patch for this
4 participants
Closes #975 and closes #342.
Changes proposed in this pull request
Document the following gotchas with BIDS datasets and QSIPrep:
Documentation that should be reviewed
https://qsiprep--1001.org.readthedocs.build/en/1001/usage.html#preparing-data-for-qsiprep