Software

Sequence software

Benedikt Poser and members of his group are well known in the field for his sequence developments. The most-popular sequence implementations are:

These tools have partly been included into SIEMENS work-in-progress (WIP) packages and can be requested directly from SIEMENS.

Other sequences have been widely shared via SIEMENS C2Ps and are available upon request.

Screenshot from 2019-02-06 09-36-27

Users of the sequence technologies developed by the MR-Methods group.

High-resolution processing scripts

These are a bunch of wrappers and scripts for accurate analysis of ultra-high-resolution fMRI. Written by Sriranga Kashyap and developed for unconventional datatypes and rely on the ANTS. It’s has been used for its routines of ultra-high resolution alignment across runs/days and the integration of motion correction, distortion correction, and co-registration into one resampling step etc. The code will be made available via Gitlab.

LAYNII

LAYNII is a collection of C++ programs designed for layer-fMRI analysis and VASO analysis. LAYNII is mostly developed by Renzo Huber and used code snippets from the AFNI-group for the nifti I/O. The name refers to analysis of LAYer-fMRI with NIfti data. LAYNII that operates exclusively in voxel-space, not in vertex space. LAYNII is designed to generate topologically consistent estimated of layers and columns with partial brain coverage data.

It can be downloaded and installed from Github.

Step-by-step instructions and example cases are provided as layerfmri.com.

sensory_motor_grid.png

The most-often used programs of LAYNII are tools to estimate layers and columns for unfolding of GM patches.

Recon Tools

The MR-Methods group uses and developed advanced reconstruction tools. Specifically Gilad Liberman developed Minimal Linear Networks (MLN) for  the reconstruction of spiral readouts.

Fig5_ReconsOnRealData-01.png

Example result of MLN reconstruction with reduced artifact levels.

The corresponding software is available on Github.

 

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