MR sequence information

  • SimNIBS relies on FreeSurfer to segment the brain and on FSL BET/BETsurf to segment the rest of the head.
  • FreeSurfer needs a good separation between the brain and the signal from the spongy bone of the skull to work well. Correspondingly, we got the best results when using MPRAGE acquistions with selective water excitation for fat suppression (spongy bone is fatty).
  • On the other hand, FSL BET/BETsurf gave poor results for the outer skull surface when having only fat suppressed images as input.
  • Without fat suppression, the positions of the spongy bone and subcutaneous fat will be displaced in the MR images due to the chemical shift artifact. This can cause slight overlaps between the brain and the spongy bone that reduces the accuracy of the skull reconstructions by FSL BET/BETsurf. In order to minimize the displacement, we use high bandwidths (both for the T1- and T2-weighted images) and thin slices with gaps in-between (for the T2-weighted images). However, both measures reduce the SNR, resulting in noisy images.

Given the above considerations we propose the following strategy:

  • When acquring two images for head reconstruction, the T1 should be acquired with fat suppression so that FreeSurfer works well. The T2 should be without fat suppression, but have thin slices with gaps and a high bandwidth. The combination of the fat-suppressed T1 and the noisy (but accurate) T2 with the spongy bone clearly visible seems to work well for FSL BET/BETsurf:

  • When acquring four images, two should be with fat suppression, and two without (but use a high bandwidth and thin slices). SimNIBS will use the fat-suppressed T1 as input for FreeSurfer. The fat-suppressed T1 and T2 images will be used to reconstruct the inner skull boundary with FSL BET/BETsurf. The normal T1 and T2 images will be used to reconstruct the outer skull boundary and the skin surface:

  • All images were acquired on a Siemens TIM Trio equipped with a 12-channel head coil.
  • The sequence parameters are described in the documentation subfolder of the SimNIBS distribution (Note: These parameters were updated and differ from the ones originally listed in Windhoff, Opitz & Thielscher, Human Brain Mapping).
version2/mri_sequences.txt · Last modified: 2015/08/05 18:12 by axel
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