From 68056b0db45c96fa519e8009abf55b23432367ea Mon Sep 17 00:00:00 2001 From: neurolabusc Date: Mon, 19 Dec 2022 10:12:20 -0500 Subject: [PATCH] Update Philips README Update Philips README (https://github.com/rordenlab/dcm2niix/issues/377) --- Philips/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Philips/README.md b/Philips/README.md index 3ac7e353..64963a12 100644 --- a/Philips/README.md +++ b/Philips/README.md @@ -152,7 +152,7 @@ Philips DICOMs do not allow one to determine the temporal order of volumes for d Likewise, the BIDS tag "PhaseEncodingDirection" allows tools like [eddy](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy) and [TOPUP](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup) to undistort images. While the Philips DICOM header distinguishes the phase encoding axis (e.g. anterior-posterior vs left-right) it does not encode the polarity (A->P vs P->A). -Another value desirable for TOPUP is the "TotalReadoutTime". Again, one can not confidently calculate this from Philips DICOMs (though on can [approximate it if you make a few assumptions](https://github.com/nipreps/sdcflows/issues/5)). If you do decide to calculate this using values from the MRI console, be aware that the [FSL definition](https://github.com/rordenlab/dcm2niix/issues/130) is not intuitive for scans with interpolation, partial Fourier, parallel imaging, etc. However, it should be pointed out that the "TotalReadoutTime" only influences TOPUP's calibrated validation images that are typically ignored. The data used in subsequent steps will not be influenced by this value. +Another value desirable for susceptibility distortion correction (e.g., TOPUP) is the "TotalReadoutTime". Be aware that the [FSL definition](https://github.com/rordenlab/dcm2niix/issues/130) is not intuitive for scans with parallel imaging, phase oversampling, partial Fourier, interpolation, etc. It has been challenging to establish and validate the correct equations to calculate "TotalReadoutTime" on Philips in the presence of all these possible factors, and the issue is further complicated by the fact that Philips have may changed the manner in which it reports the [relevant information over time](https://github.com/rordenlab/dcm2niix/issues/377#issuecomment-598665157). For this reason, for Philips data, `dcm2niix` currently reports `EstimatedTotalReadoutTime` and `EstimatedEffectiveEchoSpacing` (note the inclusion of `Estimated` as part of those variable names). See [issue 377](https://github.com/rordenlab/dcm2niix/issues/377) for a fuller discussion. However, it is also relevant to note that getting "TotalReadoutTime" correct is not critical to the TOPUP correction _if the readout time is identical for all the relevant images_ (i.e., the spin-echo EPI images to estimate the field, as well as any subsequent images being corrected). If that is not the case, or if you want TOPUP to return a valid estimate of the field itself (in Hz; `--fout` flag), then getting "Total Readout Time" correct is important. ## Partial Volumes