Processing files containing Siemens VOP data

[Chris Rodgers]

Dear Gadgetron community.

I asked at the recent Gadgetron training course about whether Gadgetron can extract the Virtual Observation Point RF monitoring information that is embedded in Siemens .dat files acquired on the 7T Terra in pTx mode (and indeed on other pTx-enabled scanners such as the Prisma). This is used for RF safety monitoring. The samples are recordings from directional couplers attached to the system transmit lines. So for example, on an 8 transmit channel system like ours there will be 8 forward and 8 reflected signals monitored during every transmit pulse.

I tested this morning with a phantom .dat file. The file and my input/output and a Matlab script to investigate it are all here https://drive.google.com/drive/folders/1KKa0uwDNNsERnJDoU905miU38A0w8JyD?usp=sharing

What I found is that Gadgetron already sees the VOP entries appear into the ISMRMRD converted file. I plotted the first channel's first VOP data and it matches up against that shown in the Siemens "MDB" tool.

However, annoyingly, the presence of these VOP lines means that gadgetron will not reconstruct the actual image from this file.

Can I ask what should be done to fix this? I presume that the siemens_to_ismrmrd converter needs adjusting so that it knows that lines with the "VOP" flag are not part of the imaging data but that they should be saved separately somehow. Perhaps saved in the same way that physio logging data is saved as you were explaining in the summer school video call.

This is not urgent, but it would be nice to get this supported cleanly in Gadgetron.

Thanks,

Chris.

[Dario Bosch]

Dear all,

Some time ago, when I experimented with Gadgetron on a Step2.3 pTx
system, I had the same problem. I came up with the following python
gadget to filter out those RT feedback lines.
I don't know if this works for Terra or if the flag assigned to those
measurements is different.

I think filtering in gadgetron is the cleanest solution, since sometimes
one might want to actually use that data.

Best,
Dario

import numpy as np
from gadgetron import Gadget

removeFlag = 138412032

class ExcludeRTfeedback(Gadget):
def process(self, head, data):
#print(head.flags)
if head.flags == removeFlag:
return 0
else:
self.put_next(head,data)
return 0

--
Dario Bosch

Max Planck Institute for Biological Cybernetics
Max-Planck-Ring 11
72076 Tübingen
Germany
Tel: +49 (0)7071 601-934

[Chris Rodgers]

Thanks Dario.

I was wondering whether it would be good to update siemens_to_ismrmrd converter so that the VOPs are brought in as waveform data. This would be similar to how syncdata are stored now, e.g. like in this branch (https://github.com/ismrmrd/siemens_to_ismrmrd/commit/683649d2b8e818250c3add1f8b4545cec8e2c49b) or this PR (https://github.com/ismrmrd/siemens_to_ismrmrd/pull/34). The reason I thought this might be more appropriate is because the VOP data are not MR imaging data in the conventional sense so they can't be reconstructed by any of the normal gadgets. But they could be really nice to have available online.

BW

C.

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