fMR Imaging

The Siemens Trio scanner offers several features for acquiring fMR imaging data.  The three main features for the scanner are:

  • Motion Correction - Generates a second set of time series data using retrospective motion correction algorithms.
  • Online Functional Maps - Generate a t-map from the fMR data based on a user defined paradigm.
  • PACE - On-line prospective motion correction of EPI images that shifts the actual acquire slice in the scanner.  Follow the images below for sample EPI series with and without PACE:

 

 

        EPI Series Acquired Without 3D PACE

            VIDEO: fMRI w/o PACE - Human Head

 

 

        EPI Series Acquired With 3D PACE

            VIDEO: fMRI w/ PACE - Human Head

 

 

The Siemens scanner has three types of image order that the user can select at the scanner console.  This selection affects the order in which slices will be acquired.  In Siemens conventions the negative direction is (Right, Anterior, Foot) and the positive direction is (Left, Posterior, Head). For axial slices, the inferior slices are collected first.  For sagittal slices, the right side of the brain is collected first. For coronal slices, the anterior part of the brain is collected first. The modes are:

  • Ascending - In this mode, slices are acquired from the negative direction to the positive direction
  • Descending - In this mode, slices are acquired from the positive direction to the negative direction
  • Interleave - In this mode, the order of acquisition depends on the number of slices acquired.
    • If there is an odd number of slices, say 27, the slices will be collected as:

      1 3 5 7 9 11 13 15 17 19 21 23 25 27 2 4 6 8 10 12 14 16 18 20 22 24 26.

    • If there is an even number of slices (say 28) the slices will be collected as:

      2 4 6 8 10 12 14 16 18 20 22 24 26 28 1 3 5 7 9 11 13 15 17 19 21 23 25 27.

This is based on information recently received from folks at Siemens (John Kirsch and Dave Purdy) and confirmed by Lee Friedman at the MIND Institute in NM with a small bottle of water and a slow interleaved EPI acquisition.

The maximum number of slices for a Siemens Gradient Echo EPI sequence is provided in the table below for different TE's and TR's:

 

Maximum Number of Slices for a BOLD Study

TR (ms) TE (ms) Max Slices
1500 30 23
2000 30 31
3000 30 45
4000 30 62
1150 40 20
2000 40 27
3000 40 40
4000 40 54
1500 50 17
2000 50 23
3000 50 35
4000 50 57

 

Number of Dummy Acquisitions for BOLD Imaging

TR (ms) Dummy Acquisitions
<1000 4
2000-4000 2
>4000 1

 

NOTE - Most of the above scanning options for the Siemens Trio Scanner are also available for the Siemens Avanto Scanner, with two exceptions. PACE imaging is not possible on the Avanto scanner. Also, for Advanced Functional Neuro, Siemens on-line fMR viewing tools are available on the console.

 

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