FAQS

Distortion correction

We recommend using FSL's Topup. An example pipeline for running topup is given on https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup Note that it is not usually necessary to calculate the readout duration (and look for parameters such as the ETL and echo spacing), because all our topup images are matched in terms of readout length to the functional or diffusion scan they are used to correct. Hence, providing a readout length of '1' will generate warp field in units of voxels rather than mm. These can be equally well to undistort the images, in exactly the same way as in the ApplyTopup example.

MP2RAGE and MP2RAGEME

MP2RAGE is a self-bias field corrected sequence for T1-weighted imaging and T1-mapping at 7T. https://www.sciencedirect.com/science/article/abs/pii/S1053811909010738?via%3Dihub. On the Philips scanners, it can be ran as a single scan (cardiac phases option, patch-free), or as two separate scans (MISS option, requires MISS patch). In the MISS version, one can included fat navigators for retrospective motion correction (See https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.25670 for more info).

Both MP2RAGE image types can be reconstructed using the MRCodeTool, either by exporting the data or with inline PRIDE jobs. The results of the Inline PRIDE jobs can be exported as dicoms or nifti's from the database as any other scan. You can also plan your next acquisitions on these images. Take the scan list view where you see the images rather than the scan names, to select the data set you want. The T1-weighted images and T1-maps are combined into a single dataset with 2 separate volumes. Scrolling through brings you from one to the other and back.

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The MP2RAGEME sequence is an extension of the MP2RAGE which includes a multi-echo image set from which we can obtain a T2* map and QSM data. A schematic overview is given in the figure above. A more complete description can be found here: https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24490 As MP2RAGEME data can only be acquired with the MISS patch, fat navigators tend to be included too. Their use in the reconstruction is not trivial and requires proper export of the .raw and .lab data, as well as the acquisition of a short reference scan. A 0.7mm protocol which works very well is provided in the standard protocols. A detailed description is provided here and motion correction results can be found here. If you need an adapted protocol, please contact the authors of these papers to discuss the options.