Siemens Twix data format

[Richard]

The Team working on Gannett (specialised gabba spectroscopy analysis) have recently implemented reading in the TWIX data format from Siemens scanners. This has the advantage of having all the FID’s stored within the data file, rather than the traditional Siemen’s averaged data.  Do you have any plans to implement this data format in Tarquin?

[Martin Wilson]

Hi Richard,

I've had this feature requested by a few people now so yes - I plan to add SVS support for twix format as it seems to becoming popular.

As a temporary measure I will write some portable code in python to convert twix to a simple format that TARQUIN can read (dpt).

Martin

On 23 Jul 2014 04:55, "Richard" <arjn...@gmail.com> wrote:

The Team working on Gannett (specialised gabba spectroscopy analysis) have recently implemented reading in the TWIX data format from Siemens scanners. This has the advantage of having all the FID’s stored within the data file, rather than the traditional Siemen’s averaged data.  Do you have any plans to implement this data format in Tarquin?

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[Richard]

Excellant,

 

Thanks greatly

 

On Wednesday, July 23, 2014 3:54:01 PM UTC+10, Martin Wilson wrote:

Hi Richard,

I've had this feature requested by a few people now so yes - I plan to add SVS support for twix format as it seems to becoming popular.

As a temporary measure I will write some portable code in python to convert twix to a simple format that TARQUIN can read (dpt).

Martin

On 23 Jul 2014 04:55, "Richard" <arjn...@gmail.com> wrote:

The Team working on Gannett (specialised gabba spectroscopy analysis) have recently implemented reading in the TWIX data format from Siemens scanners. This has the advantage of having all the FID’s stored within the data file, rather than the traditional Siemen’s averaged data.  Do you have any plans to implement this data format in Tarquin?

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[Qizhu_Wu]

Hi Martin,

When loading in Siemens MEGA-PRESS rda data, the option 'Dynamic averaging' in the 'Data parameters' tab seems not useful as the rda is already averaged. Although we could save IMA or DICOM data for each individual scan, they are separate files that could not be imported together. 

Is this feature designed for other MRI vendor?

Regards

Qizhu Wu

On Wednesday, July 23, 2014 3:54:01 PM UTC+10, Martin Wilson wrote:

Hi Richard,

I've had this feature requested by a few people now so yes - I plan to add SVS support for twix format as it seems to becoming popular.

As a temporary measure I will write some portable code in python to convert twix to a simple format that TARQUIN can read (dpt).

Martin

On 23 Jul 2014 04:55, "Richard" <arjn...@gmail.com> wrote:

The Team working on Gannett (specialised gabba spectroscopy analysis) have recently implemented reading in the TWIX data format from Siemens scanners. This has the advantage of having all the FID’s stored within the data file, rather than the traditional Siemen’s averaged data.  Do you have any plans to implement this data format in Tarquin?

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[Talitha]

Hi Martin,

Is there any update on the TWIX .dat format from Siemens?

I have this data and have run it in Gannet, though I am interested in looking at the correlation with a Tarquin analysis.

Cheers,

Talitha

On Wednesday, 23 July 2014 15:54:01 UTC+10, Martin Wilson wrote:

Hi Richard,

I've had this feature requested by a few people now so yes - I plan to add SVS support for twix format as it seems to becoming popular.

As a temporary measure I will write some portable code in python to convert twix to a simple format that TARQUIN can read (dpt).

Martin

On 23 Jul 2014 04:55, "Richard" <arjn...@gmail.com> wrote:

The Team working on Gannett (specialised gabba spectroscopy analysis) have recently implemented reading in the TWIX data format from Siemens scanners. This has the advantage of having all the FID’s stored within the data file, rather than the traditional Siemen’s averaged data.  Do you have any plans to implement this data format in Tarquin?

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[Martin Wilson]

Hi Talitha,

I have some code - but I think it needs more testing. Could you send
me an example dataset so I can check (TWIX data can be quite large so
you might need to use something like dropbox).

Martin

On 4 September 2015 at 08:29, Talitha <talith...@gmail.com> wrote:
> Hi Martin,
>
> Is there any update on the TWIX .dat format from Siemens?
> I have this data and have run it in Gannet, though I am interested in
> looking at the correlation with a Tarquin analysis.
>
> Cheers,
> Talitha
>
>
> On Wednesday, 23 July 2014 15:54:01 UTC+10, Martin Wilson wrote:
>>
>> Hi Richard,
>>
>> I've had this feature requested by a few people now so yes - I plan to add
>> SVS support for twix format as it seems to becoming popular.
>>
>> As a temporary measure I will write some portable code in python to
>> convert twix to a simple format that TARQUIN can read (dpt).
>>
>> Martin
>>
>> On 23 Jul 2014 04:55, "Richard" <arjn...@gmail.com> wrote:
>>>
>>> The Team working on Gannett (specialised gabba spectroscopy analysis)
>>> have recently implemented reading in the TWIX data format from Siemens
>>> scanners. This has the advantage of having all the FID’s stored within the
>>> data file, rather than the traditional Siemen’s averaged data. Do you have
>>> any plans to implement this data format in Tarquin?
>>>
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[Enrico M De Vita]

Dear Martin,

I was wondering if there has been any progress on this (converting Siemens TWIX containing multiple acquisitions to .dpt)?
 I'd be happy to collect some test data if you have not got any yet.

thank you!

Enrico
e.de...@ucl.ac.uk
--
Enrico De Vita, PhD
Senior Clinical Scientist (MR Physics)
National Hospital for Neurology and Neurosurgery
Queen Square, WC1N 3BG, London
Honorary Senior Lecturer
UCL Institute of Neurology
London
+44 20 3448 3130

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[Philipp Ehses]

Hi Martin,

I just stumbled over this thread and wanted to let you know that there are already a few tools available for reading in TWIX data.

Gannet uses a matlab-script (mapVBVD.m) which was developed by myself. I also have a very basic and also a bit outdated version in python in case you're interested (I'll have to check&update the python code if you're interested).

Another option would be to use Michael Hansen's excellent "siemens_to_ismrmd"-convertor (https://github.com/ismrmrd/siemens_to_ismrmrd; free & open-source c++-code) which converts the twix-file into a HDF5-library-file (the layout of which is described here: https://ismrmrd.github.io/). There's a python library called h5py that can read HDF5 files.

Philipp

[Martin Wilson]

Hi Philipp,

Thanks for reminding me about this, I did write a small application a
while back (mainly based on your MATLAB code) that converts twix to
dpt format. Not particularly well tested, but I've attached it on the
off chance that someone finds it useful...

Also thanks for the links, I wasn't aware of the ismrmd format.

Martin

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[Suo Chao]

Hi Martin,

Thanks for sharing.

I can successfully run the script to convert data from a siemens Skyra (VD 13) scanner.

Just have two questions:

1, what does the "Block size" refer to?

2, how does the script average the signals across different coils and repeats? is there any correction/tuning/quality-controlling on each individual signal before averaging?

Thanks,

Chao

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[Martin Wilson]

Hi Suo,

Block size is the number of dynamic scans to average over. So if there
are 128 original dynamics, a block size of 4 will result in an output
of 32 where the first dynamic is the average of 1-4, the second
dynamics is the average of 5-8...

Coils are averaged by phasing to the first data point in the FID and
also scaled by the magnitude of the first point.

No frequency correction or anything like that prior to averaging.

Martin

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