7T sLASER Basis set

Analysis / Modeling Basis Sets
1

Hi All,

Wanted to see if someone happened to have an sLASER basis set for 7T Siemens data with a TE of 35 floating around out there or is someone might be able to point me to creating one. I’m a newbie on basis set generation and have not done that before.

Best,
Jessica

2

My best guess is @wclarke might be able to help, I think Oxford has a 7T Siemens magnet. Where’d you get the sequence from? Is this product?

3

Thanks for the speedy response! We got it from CMRR.

4

Have you asked them whether they have one? :slight_smile:

5

Indeed we have :slight_smile: I’ll update if I get one.

6

Hi Jessica,

I have some code to generate basis sets for both sLaser sequences from CMRR. If you shared the protocol pdf I could probably generate one for you.

Will

1 Like
7

Hi eveyone
Is there any open source code that allows you to generate basis set for any sequence any field strength any TE?

Is there anyone who can direct me to apaper that makes me understand these basis sets?
I am a newbie in the MRS analysis.

Thank you so much.
Best
Shah

8

There are several tools available, but I’m not sure that they tick all of the boxes you want.
MRSCloud has options to simulate a whole bunch of sequences (not any sequence though, the most common ones). The source code lives at shui5/MRSCloud: MRS Simulation (github.com).
FSL-MRS also has on-board simulation tools, as does VeSPA; MARSS probably gives you the most freedom to specify the sequence of events, but it is not open-source - you can look through the Software category on MRSHub to learn about all the tools that are out there.

However, in order to use these tools, you will need to have exact knowledge of your sequence parameters (e.g. the timings of all the pulses as well as their exact waveforms). This knowledge is unfortunately not often available to non-expert users, since it often requires research agreements with the vendors to access their code. I guess it depends a little bit what you need to do - if you need to simulate a particular sequence that you are using, you might need to get in touch with some experts in this forum, but if you just want to learn how these simulators work, then any of the open-source tools above will be a good learning training ground.

Cheers,
Georg

Edit: A couple papers:
MRSCloud: A cloud‐based MRS tool for basis set simulation - Hui - 2022 - Magnetic Resonance in Medicine - Wiley Online Library
Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation - Landheer - 2021 - NMR in Biomedicine - Wiley Online Library

1 Like
9

Great. very useful information.
MRSCloud was amazing. Thanks for introducing.

Best
Shah

1 Like
10

Hello Mr @wclarke,

Do you have sLASER basis set for Siemens 7T data also a TE 5 and 135? or can you help me create one please. I am also a novice when it comes to generating basis sets.

Thank you very much,

Have a nice day,

Landoline

11

Hi @lbonnin,

I have code online for the sequence eja_svs_slaser, available from CMRR. That link contains python code for generating a sequence description for any echo time that can then be simulated using FSL-MRS’s basis set simulation tool.

5 Likes
12

Bookmarking that… :wink:

13

I have others as well, but need to work my way through them tidying up. Some also only work with fixed echo time because I haven’t worked out the logic.

14

@admin This is the sort of thing I was saying (in Lausanne last year) that we should incorporate into the cloud simulator that you guys have made.

15

Thank you very much for your help. Do you have a tutorial for installing FSL-MRS with a linux WSL under windows please?

Have a nice day,

lbonnin

16

FSL-MRS is pretty much pure python, so you can install it either natively or using conda on WSL.

Alternatively you can get all the tools with a full FSL install see FslInstallation/Windows - FslWiki

17

Sorry all… this is probably a silly question and has an easy answer but is there a way to convert the .json basis files into a .basis for LCModel?

18

There are options in fsl_mrs_sim to generate the required outputs to use the LCModel makebasis function. See fsl_mrs/scripts/fsl_mrs_sim.py · master · FSL / fsl_mrs · GitLab and fsl_mrs/scripts/fsl_mrs_sim.py · master · FSL / fsl_mrs · GitLab . I have to admit it’s been so long since I used the options that I can’t remember what the LCModel .IN file is or what the location that you have to enter would be.

19

Will this was super helpful!!! Do you happen to have the same thing for STEAM at 7T TE 20??