BIDS metadata for MP2RAGE data

bids
mp2rage

#1

Hi guys,

I’m currently working on a small Python package (pymp2rage) that can estimate T1 (and T2*) maps based on the (ME-)MP2RAGE sequence (Marques et al, 2010).

I think it would be very useful if this package can take a BIDS-folder containing the two magnitude and phase images corresponding to the first and second inversion time. I was happy to find the BIDS Extension Proposal 1 (BEP001) which answers most of my questions.

One open question for me is if there is a BIDS metadata-field that you can use to indicate the range of intensity values in the image file that corresponds to [0, 2*pi]. Is there such a field? Or should the data be in float and just range from 0 to 6.28…? I notice that for example fmriprep just computes the entire range of unique values for a phase difference image and then assumes that this range corresponds to 2 pi, but there must be a more elegant approach, right?

Another question for me is how to organize all the metadata that is necessary for fitting the T1 maps.

The matlab scripts from José Marques need the following parameters:

MP2RAGE.B0=7;           % in Tesla
MP2RAGE.TR=6;           % MP2RAGE TR in seconds 
MP2RAGE.TRFLASH=6.7e-3; % TR of the GRE readout
MP2RAGE.TIs=[800e-3 2700e-3];% inversion times - time between middle of refocusing pulse and excitatoin of the k-space center encoding
MP2RAGE.NZslices=[35 72];% Slices Per Slab * [PartialFourierInSlice-0.5  0.5]
MP2RAGE.FlipDegrees=[4 5];% Flip angle of the two readouts in degrees
MP2RAGE.filename='MP2RAGE_UNI.nii' % fi

I would translate this into BIDS as follows:

  • B0 can go into MagneticFieldStrength
  • TR can go into RepetitionTime
  • TRFLASH: No correponding BIDS field? One option would be to put the TR_flash in RepetitionTime and put TR minus TRFLASH in the BIDS field DelayTime
  • TI can go into InversionTime
  • NZslices: NumberShots and PartialFourier?
  • FlipDegrees: FlipAngle

Cheers,
Gilles

Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., van de Moortele, P.-F., & Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. NeuroImage, 49(2), 1271–1281. http://doi.org/10.1016/j.neuroimage.2009.10.002


#2

Thanks for bringing this up! MP2RAGE is covered by BEP001, but the scanning parameters you mentioned are not included. It would be a great addition!

More generally I think the issues you raised would benefit from more exposure to people on the bids-mailing list could you post it there?