Dear all,
First, thank you for providing fmriprep - very useful!
I have questions about ESS and TRT for SDC of bold fMRI with a B0 fieldmap using Philips data.
In the documentation of fmriprep SDC and source code of fmriprep.interfaces.fmap there are the functions get_ees and get_trt. For Philips data it seems to be enough to define the WaterFatShift, MagneticFieldStrength, PhaseEncodingDirection and ParallelReductionFactorInPlane to calculate ess and trt.
First question:
a) does this signify that the EffectiveEchoSpacing does not need to be specified in the BIDS json file of the bold fmri, when WaterFatShift, MagneticFieldStrength, PhaseEncodingDirection and ParallelReductionFactorInPlane are given in the json file?
b) this then gives a warning in the bids-validation step ("You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible.") that can be safely ignored?
Second Question:
a) looking at the source code:
-
if wfs is not None:
fstrength = in_meta['MagneticFieldStrength']
wfd_ppm = 3.4 # water-fat diff in ppm
g_ratio_mhz_t = 42.57 # gyromagnetic ratio for proton (1H) in MHz/T
wfs_hz = fstrength * wfd_ppm * g_ratio_mhz_t
return wfs / (wfs_hz * etl)
-
it seems that ParallelReductionFactorInPlane (the sense acceleration) is not used?
b) this ParallelReductionFactorInPlane is not used, since the echo-train-length (etl) in Philips images is already taking this into account? Correct?
c) I'm confused by other information on the web (among others: http://www.spinozacentre.nl/wiki/index.php/NeuroWiki:Current_developments#B0_correction) that also provide a calculation for the ESS as:
effective echo spacing = (((1000 * wfs)/(434.215 * (EPI factor+1))/acceleration)
Thus here 'acceleration' is used. Acceleration means the sense factor, which is also the same as the ParallelReductionFactorInPlane? Correct?
I guess it all depends on how 'etl' is defined. In the philips definition it already incorporates the ParallelReductionFactorInPlane (etl = NumberOfPhaseEncodingSteps/ParallelReductionFactorInPlane)
Last Question:
Starting from Philips dicom, I need to extract the correct information to put into the BIDS json file.
Using matlab dicominfo to extract relevant information out of Philips Dicom, one finds the following:
- MagneticFieldStrength in 'MagneticFieldStrength'
- etl in 'Private_2001_1013'
- WaterFatShift in 'Private_2001_1022'
- ParallelReductionFactorInPlane in 'Private_2005_140f.Item_1.ParallelReductionFactorInPlane';
EffectiveEchoSpacing is not in the philips dicom header, and is thus calculated.
Hope someone can help with (part of) my questions...
Best regards,
Stefan
Ps. Slightly of topic:
The PhaseEncodingDirection is not fully specified in the philips dicomheader? One cannot find e.g. 'j' or 'j-' as both are defined as 'COL' in the philips dicom header?
Also the slice timing info is not in the philips dicom header?
However ParallelReductionFactorOutOfPlane is specified in the philips dicom header, and this corresponds to the multiband factor?
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