The possibility of integration to Bruker API

[amirshamaei]

Thanks for making your code open source. We are working on Bruker API package providing I/O interface for Bruker data sets. I measured some EPI datasets as well and we are about to implement reading them into our API. I was wondering if it is possible to collaborate for integration. In addition, We tried to implement EPSI sequence but I am curious how you implemented it? and How did you store phase data as a separate folder? currently, we have only access to raw data(complex data) I appreciate in advance,

[ViswanathLab]

Hi Amir,

What do you mean by collaborate? We have made the code publicly available, so you can use it as long as you reference our work in any related work.

I have not implemented the EPSI myself. It is part of the ParaVision 6 from Bruker. Regarding the phase data, after the acquisition you can duplicate the data processing/reconstruction and select to create and save them as phase (what PV version are you using?). But as long as you have the complex data, that is even better – you don’t need the phase.

Best, Georgios

From: Amir Shamaei @.> Reply-To: ViswanathLab/EPSI @.> Date: Wednesday, August 4, 2021 at 6:39 AM To: ViswanathLab/EPSI @.> Cc: Subscribed @.> Subject: [ViswanathLab/EPSI] The possibility of integration to Bruker API (#1)

Thanks for making your code open source. We are working on Bruker API package providing I/O interface for Bruker data sets. I measured some EPI datasets as well and we are about to implement reading them into our API. I was wondering if it ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd

Thanks for making your code open source. We are working on Bruker API package providing I/O interface for Bruker data sets. I measured some EPI datasets as well and we are about to implement reading them into our API. I was wondering if it is possible to collaborate for integration. In addition, We tried to implement EPSI sequence but I am curious how you implemented it? and How did you store phase data as a separate folder? currently, we have only access to raw data(complex data) I appreciate in advance,

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[amirshamaei]

What do you mean by collaborate?

I was wondering if you provide us with a sample dataset, then we can add the parameters to read the EPSI data in our API.

I have not implemented the EPSI myself. It is part of the ParaVision 6 from Bruker.

So, to the best of my understanding, you are using Bruker standard EPSI which does not have OVS and WS.(edited: I notice you used it for 31C measurement)

Regarding the phase data, after the acquisition you can duplicate the data processing/reconstruction and select to create and save them as phase (what PV version are you using?). But as long as you have the complex data, that is even better – you don’t need the phase.

We have PV7. Indeed I didn't know how to store the phase. RAW complex data(fid) is not processed, so most of the time another step is required which in the case of EPSI is cumbersome(i am not sure about the order of channel, average, and segments). I will try to save the phase as well. Thank you again,

[ViswanathLab]

Hi,

please find a dataset in the following link: https://ucsf.box.com/s/e4947q2fg5vuoy7gpbcu89tbunum3h34 (Let me know if the link works)

Yes, in hyperpolarized 13C-MRSI we do not need OVS or WS and the TR is short. Also we don't have any signal averages.

The Bruker software helpline can answer many of the question regarding the order of channel, average, and segments. Not sure if PV7 is different from PV6, so I cannot answer with certainty. I am using the data reconstructed by Bruker instead of the raw data, as there is the need to use the Bruker reconstruction for eddy currents and trajectory corrections.

[amirshamaei]

@ViswanathLab Thank you. I got the data and I will include it in our API.