MP2RAGE: challenges and artifacts of its use for layer-fMRI

The MP2RAGE sequence is very popular for 7T anatomical imaging and is very commonly used to acquire 0.7-1 mm resolution whole brain anatomical reference data. Aside of this common application, it can also be very helpful for layer-fMRI studies to obtain even higher resolution T1 maps in the range of 0.5mm iso. However, when optimizing MP2RAGE sequence parameters for layer-fMRI studies, there are a few things that might be helpful to keep in mind.

In this post, I would like to discuss the challenges of using the popular MP2RAGE sequence in layer-fMRI studies. Specifically I will discuss challenges/features regarding:

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Installing ISIS-conv on MAC

ISIS-conv is a very useful dicom to nii converter from Enrico Reimer. ISIS-conv gets along with a lot of challenging data sets that no other converter (that I know of) can handle so conveniently:

  • SMS-data, where individual slices have a non-constant inter-slice distances.
  • VASO data with non-constant TRs
  • Multi-echo, multi-coil, and Magnitude/Phase data.

There is a Mac-installation package of ISIS-conv. Unfortunately, however, with every IOS update, it has become more complicated to install it.

Since, I spend too much time figuring out how to install it after every update, I am collecting the necessary steps in this Blog post for future reference:

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Gradient Temperature

tSNR changes across time

I got interested in gradient temperature because of the weird effect that tSNR seemed to increase over time.

Upon posing this effect on Twitter, PracitalfMRI and Ben Poser suggested that it might be due to gradient temperature. So I learned how to track it with as described below.

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