User Guide

IT Support

For topics such as remote access using VNC, accessing MGB resources using VPN, and more: https://it.martinos.org/

MRI Operations

For general information about the Martinos Technology core and MRI/PET/TMS operations: https://mri.martinos.org/

For any specific questions about the Connectome 2.0 MRI system, please email us at connectome2@mgh.harvard.edu.

GitHub Links

For any questions, please use the Discussions forum under our lab group’s GitHub repository QandA, and a member from our lab will assist.

Sequence Capabilities

Below are pulse sequences that are either available or in development for use on the Connectome 2.0. 

 Pulsed gradient spin echo (PGSE) diffusion-weighted 2D EPI sequence written in Siemens IDEA for Connectome 2.0 XA61 software version and integrating the following functions:

  1. Expert control over diffusion times and gradient strength
  2. Output of magnitude and phase images to enable acquisition of complex-valued diffusion MRI data
  3. Integrated triggers for use with Skope field probes

PGSE 3D EPI sequence written in Siemens IDEA (XA61) with full online reconstruction and multi-shot capabilities

Romer-EPTI is a novel acquisition that can achieve significantly improved SNR efficiency while comprehensively addressing various challenges—providing distortion-free imaging, minimal spatial blurring, motion robustness, and simultaneous multi-TE imaging. It has been demonstrated to achieve distortion-free whole-brain in-vivo diffusion MRI at mesoscale resolutions on both clinical 3T (500-μm iso) and 7T (485-μm iso) scanners, with additional improvements on the Connectome 2.0 scanner. Romer-EPTI also demonstrated high SNR gain and robustness in high b-value (b = 5000 s/mm2) and time-dependent dMRI at standard spatial resolutions. (Details see https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.30365). Current stage: The sequence and reconstruction for the C2.0 scanner are currently under development and testing. It will be available to users through collaboration with the development team or through a C2P agreement in the future. 

OGSE (Oscillating-Gradient Spin-Echo) sequence provides sensitivity to microstructures features at shorter diffusion times compared to conventional PGSE (Pulsed Gradient Spin Echo) sequence. It is encoded with trapezoid-cosine diffusion gradient and uses 2D echo planar read out (ep2d_diff_ogse.dll, libep2d_diff_ogse.so). Gmax and SRmax can be set up to 500 mT/m and 600 T/m/s, respectively. Additional to the features of 2D EPI diffusion sequence (ep2d_diff), user can modulate oscillation frequency (step size = 5 Hz, range = 30 – 100 Hz), number of periods (N=1, 2, 3), and mixing time (minimum = 7.34 ms, range varies by frequency and number of periods) in the UI. 

gSlider for high-resolution diffusion imaging. IDEA sequence (with online reconstruction) for VE and XA baselines is available on martinos.org/c2p 

PRIME (phase reversed interleaved multi-echo) sequence enables distortion free, high resolution diffusion imaging. It uses the dead time in gSlider encoded acquisitions to sample additional spin echoes without altering the scan time. This can be used in two different ways: (i) for mesoscale acquisitions, the second echo can be acquired at lower resolution to serve as a shot-to-shot phase, B0 and motion navigator. (ii) at moderate (e.g. 1 mm isotropic) resolutions, multiple spin echoes can be sampled for efficient diffusion-relaxometry and advanced gray/white matter modeling (e.g. multi-echo NODDI/SANDI). The sequence is implemented in Pulseq and sequence and reconstruction code are available on GitHub. There are readily available sequences compiled at 490 um, 680 um and 1 mm isotropic resolutions sampling multiple shells.