feat: Add flag to fallback to Estimated* metadata or a passed value for TotalReadoutTime #3423
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May 15, 2025
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Will merge on pass unless stopped. |
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25.1.0 (May 21, 2025) New feature release in the 25.1.x series. This release includes a small fix related to interpolations on the bounds of the image field-of-view. This improves consistency with prior versions of fMRIPrep for data with limited fields-of-view or small bounding boxes. This release also adds support for providing fallback values for ``TotalReadoutTime`` metadata. For Philips datasets, if ``EstimatedTotalReadoutTime`` or ``EstimatedEffectiveEchoSpacing`` are available, you can use these by passing ``--fallback-total-readout-time estimated``. For datasets with no readout time information, a numeric value can be passed, for example, ``--fallback-total-readout-time 0.05``. If the readout time information is known, it is preferable to encode directly in the dataset, but there are cases where it is better to explicitly pass the value to the software than inject uncertain metadata into the dataset. In particular, the true readout time is not necessary for SyN-SDC, but a value is nonetheless needed in order to estimate the inhomogeneity field. This release is a long-term-support *candidate*. We will be performing extensive tests and monitoring bug reports over the next couple of months to determine whether issues can be addressed without making breaking changes. Structural processing changes ----------------------------- This release pins a version of sMRIPrep (0.18) that correctly handles precomputed tissue probability maps. The FAST segmentation also now skips an internal bias field correction step that is redundant with ANTs N4 correction, and may be inappropriate for non-human populations. Fieldmap processing changes --------------------------- This release pins a version of SDCFlows (2.13) that includes several improvements to the SyN-SDC method. In particular, the fieldmap prior that constrained the scope of displacements was reintroduced and refined. All merged pull requests ------------------------ * FIX: Use nearest mode for extrapolating data outside image boundaries (#3453) * ENH: Replace c3d_affine_tool with a ConvertAffine interface (#3464) * ENH: Add flag to fallback to Estimated* metadata or a passed value for TotalReadoutTime (#3423)
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This flag provides two additional ways to retrieve TotalReadoutTime. If
EstimatedTotalReadoutTimeorEstimatedEffectiveEchoSpacingare defined, the user can pass--fallback-total-readout-time estimatedto direct fMRIPrep to use these.This could be turned on by default, but I don't think this is prudent. The reason that
dcm2niixdoes not simply sayTotalReadoutTimeorEffectiveEchoSpacingis not to misrepresent the confidence that these are correct. Previously, users had to actively remove theEstimatedto accept the estimates, and I don't think we want to eliminate the conscious decision. However, we can make it so that users do not need to modify their datasets to accept them.Closes #3009.