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 Compressed Sensing Multiplicative (CoSeM)  denoising starts from a fully sampled 2D MR data set, discards random indirect-domain points, and makes up for these missing data by a compressed sensing reconstruction of the incompletely sampled 2D data set. This procedure is repeated for multiple renditions of the masked data –some of which will have been more strongly affected by multiplicative t1-noise than others – which then by following selection criteria can result in a 2-3 fold SNR increase, thus attenuating multiplicative noise.
This package contains the Matlab codes for Compressed Sensing Multiplicative (CoSeM) denoising which can be applicable for multidimensional NMR, MRS, and MRI, a sample dataset, as well as a short tutorial, while Compressed Sensing is implementing while resorting to the BART Toolbox implementation (https://mrirecon.github.io/bart/).

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

Sensitivity-enhanced heteronuclear NOESY experiments detecting imino-imino and imino-amino correlations for Bruker spectrometers

This package contains HETeronuclear MAgnetization Transfer (HETMAT) NOESY experiments, a heteronuclear-resolved version of NOESY experiments, demonstrated on nucleic acids. This method can enhance the resolution of homonuclear NOESY experiments by targeting selected 1H-15N spin pairs, leading to a pseudo-3D version of HSQC-NOESY. By utilizing magnetization transfers between the aqueous solvent and the imino protons on the nucleic acid, the sensitivity of cross-peaks between imino-imino and imino-amino protons can be enhanced by ≈2-5x as compared with conventional 2D NOESY counterparts. The parameter sets, sequence, MATLAB scripts, and instructions for use are included.

download HETMAT-imino-NOESY.zip

 

Extended Hadamard scheme for the acquisition of sensitivity-enhanced pseudo-2D and 3D NOESY experiments detecting imino-imino and imino-amino/aromatic correlations on RNAs (Bruker spectrometers)

This package contains Hadamard-encoded Magnetization Transfer (HMT) and Hadamard-encoded HETeronuclear MAgnetization Transfer (HETMAT) NOESY experiments implemented based on the extended Hadamard scheme. Regular Hadamard scheme fails to detect NOE correlations within the same pools of labile protons such as imino-imino correlations on RNAs. This limits the applications of the Hadamard experiments only for detecting these correlations between different pools such as imino→amino protons on RNAs, or NH→CH protons in proteins. The extended version of the Hadamard matrix solves this problem, allowing obtain artifact-free correlations both within the labile spin pools and between labile and non-labile protons. Thanks to Hadamard multiplexing, up to x6 higher SNR/unit time is achieved compared to the non-Hadamard experiment. Compared to the conventional counterpart, sensitivity gains per unit time are about an order of magnitude, revealing additional cross-peaks. All these experiments work on Avance NEO Bruker consoles. Since setting up these experiments 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 Extended-Hadamard-imino-NOESY.zip

Software package for a denoising method for multidimensional magnetic resonance spectroscopy and imaging based on Compressed Sensing

Compressed Sensing Multiplicative (CoSeM)  denoising starts from a fully sampled 2D MR data set, discards random indirect-domain points, and makes up for these missing data by a compressed sensing reconstruction of the incompletely sampled 2D data set. This procedure is repeated for multiple renditions of the masked data – some of which will have been more strongly affected by multiplicative t1-noise than others – which then by following selection criteria can result in a 2-3 fold SNR increase, thus converting multiplicative into additive noise.
This package contains the Matlab codes for Compressed Sensing Multiplicative (CoSeM) denoising which can be applicable for multidimensional NMR, MRS, and MRI, a sample dataset, as well as a short tutorial, while Compressed Sensing is implementing while resorting to the BART Toolbox implementation (https://mrirecon.github.io/bart/).

download CoSeM_denoisingcode.zip

Randomized Composite-Pulse Decoupling for Heteronuclear Saturation Experiments

Cyclic decoupling schemes can lead to strong effects associated to decoupling-sidebands in saturation transfer experiments. These can be dealt with using noise decoupling. But a much more efficient and broadbanded decoupling is achieved by randomizing the power levels/pulse lengths of a train made up by [90x-180y-90x] composite pulse inversions. A script to create such pulse lengths in a more user-friendly fashion using Bruker’s au language has also been written, and can be downloaded (at the user’s responsibility) from the link below.

Download deposit_rand_dec.zip

A package for installing multi-echo steady-state free precession (ME-SSFP) (in Bruker Paravision 6.0), and chemical shift imaging SSFP (CSI-SSFP) (in Bruker Paravision 6.0 and Bruker Paravision 360 V3.3) designed for sensitivity-enhanced Deuterium Metabolic Imaging (DMI)

This package encompasses the ME-SSFP and CSI-SSFP methods developed for Bruker MRI systems. The method comprises standard ME-SSFP, weighted average ME-SSFP, and CSI-SSFP techniques. The methods were designed to separate HDO, glucose and lactate peaks, though Glx resonances can also be resolved. Offset and echo times need to be suitably chosen, depending on the field strength. The offline reconstruction can be performed using our spectral separation tools, which are accessible for download on this page (below).

ME-SSFP_and_CSI-SSFP_sequences_and_manuals.zip

Contact: elton.montrazi@gmail.com / https://github.com/montrazi

A Matlab package for running the regularized kinetics spectral reconstruction (RK-SpecRecon) and subspace–constrained kinetic spectral reconstruction (SK-SpecRecon). These tools are specifically designed for the separation of metabolic spectral images from ME-SSFP and CSI-SSFP experiments within the context of DMI (see sequences above)

This package includes the Matlab script files required to run RK-SpecRecon and SK-SpecRecon on ME-SSFP and CSI-SSFP datasets acquired in Bruker magnets.

pro_DMI_SSFP_RK_SK_SpecRecon-main_Aug2023.zip

Contact: elton.montrazi@gmail.com / https://github.com/montrazi

Cross-polarization schemes (L-WURST-CP and TAPF-CP) for improved heteronuclear transfers involving labile protons in biomolecular solution NMR (Bruker spectrometers)

Traditional INEPT-based experiments face challenges with 1H→15N transfers due to solvent exchanges. Our approach leverages the Hwater→HN exchange process to enhance the 1H→15N transfer. However, fulfilling the required spin-locking conditions can be demanding, especially with today's power-limited cryogenic probes. New CP variants, including frequency-swept and phase-modulated pulses, are designed to address these challenges. Both theoretical and experimental performance assessments are conducted on compounds like urea, amino acids, and intrinsically disordered proteins. These strategies offer improved results compared to existing methods, especially in high-field NMR conditions.

This package contains pulse sequences, related wavemaker files, and short instructions for setting up these experiments. Also, Spinach codes are included.

cps.zip

Contact: jiiiihyun@gmail.com