Software

A package for installing SPEN in VNMRJ

The following script will install the multi-shot, multi-slice, multi-array SPEN method  on your VNMRJ system

download .zip file / download .7z file
System requirements: Linux 32 or 64 bits (64 bits recommended)
Software requirements: Agilent@VNMRJ3.2
Contact zhiyong.zhang@weizmann.ac.il or zhiyongxmu@gmail.com

To install the package, use the terminal command ( sh /package directory/SPENmsinstall.sh ) then open VNMRJ

If no matlab MCR v82 is installed, the package need super-user permission to install the matlab MCR v82.
 

A package for installing xSPEN in VNMRJ

 The following package installs the single-shot cross-term spatiotemporal encoding (xSPENss) sequence, which supports multi-slicing, segment imaging, array imaging, diffusing etc

download .zip file / download .7z file

 System requirements: Linux 32 or 64 bits (64 bits recommended), Sequence was tested in VNMRJ3.2 and VNMJ4.0. For on-line processing, the sequence requires the matlab MCR v82, which should be downloaded from MATLAB website during the installation with root permit.

Contact: zhiyong.zhang@weizmann.ac.il  or zhiyongxmu@gmail.com

 

A package for installing SPEN in Bruker Paravision 5.1

This package contains a SPEN method developed for Bruker MRI systems. The method
includes single-shot single-slice SPEN, multi-slice SPEN and RASER. Diffusion and
CEST1 weighting can be added while high-resolution imaging can be performed using interleav-
ing/segmented acquisition. An online reconstruction takes care of the acquired data and display

the images and ADC maps directly in Bruker Paravision.

download .zip file  / download .7z file

Contact: tangi.roussel@gmx.com

 

A Matlab package for running the PRO-SLAM reconstruction of 13C CSI data 

This package includes matlab script files required to run the PRO-SLAM reconstruction on CSI datasets acquired in Bruker magnets. Make sure that all these files are in the Matlab path before executing the main script.

download .zip file

Contact: gilf2305@gmail.com

 

SPEN  method  on  Bruker  Paravision  6.0x

This package contains a fully T2* refocused version of the SPEN method based on a 180° chirp pulse developed for Bruker MRI systems running Paravision 6.0 on Avance III/IIIHD systems. The method allows single-shot or interleaved/segmented acquisition with single-slice, multi-slice 2D or 3D phase encoded acquisitions, diffusion encoding, CEST weighting, and multi echo acquisitions. The sequences work – but of course, as usual, use is the operator’s responsibility

.

User instructions CentOS 5 package CentOS 7 package

Contact: Maxime Yon maxime.yon@weizmann.ac.ilmaxime.yon@gmail.com

 

Matlab package for the reconstruction of SPEN data acquired on Siemens scanners

This package is intended for immediate processing of data acquired on Siemens Prisma 3T scanner, but should be applicable to data acquired on any other scanner with appropriate modifications of the pipeline's data reading and ordering blocks.

download .zip file

download sample data

Contact: martins.otikovs@weizmann.ac.il

 

A package combining Diffusion Tensor Distribution Imaging with SPEN MRI for Bruker Paravision 6

This package contains a fully T2* refocused SPEN method allowing Diffusion Tensor Distribution (DTD) imaging as published in "Diffusion tensor distribution imaging of an in vivo mouse brain at ultra-high magnetic field by spatiotemporal encoding, NMR in Biomed 2020". The method allows single-shot or interleaved/segmented acquisition with single-slice, multi-slice 2D or 3D phase encoded acquisitions. The sequences work – but of course, as usual, their use is the operator’s responsibility.

download .zip file

Contact: Maxime Yon maxime.yon@gmail.com

Fast, sensitivity-enhanced 2D NOESY experiments targeting labile protons for Bruker spectrometers

This link contains Hadamard-encoded Magnetization Transfer (HMT) and Selectively-encoded Magnetization Transfer (SMT) experiments that were developed by graduate student Mihajlo Novakovic and Dr. Eriks Kupce. The new pulse sequences / processing macros were originally developed for nucleic acid (specifically, SARS’s RNA) research; with the aim of sensitizing (usually by ~4x) and speeding-up (usually by ~10x) 2D NOESY experiments between imino —> amino/aromatic protons (the HMT), and within the imino protons (the SMT) of the RNAs. Of course, the sequences also will work equally efficient for NH—>CH, NH—>NH and OH—>CH correlations in other suitable molecules - the important thing is to target the labile 1Hs in the F1 dimension, using their 1D 1H spectrum as starting point. The packages contain parameters sets, sequences, all au programs for creating its pulses and the data processing, and instructions for use. The HMT version includes a looped inversion option without and with 15N filter and Watergate. THe SMT is CW- saturation based. HMT works on both Avance III and NEO Bruker consoles, and SMT works best on Avance NEO (due to memory issues with the Avance III). Since setting up SMT the first time can be tricky, people are welcome to contact us with their questions. As usual, users should proceed with care and at their own risk.

download HMT Imino with decoupling.zip

download Selective MT Imino.zip