problem with siemens raw data conversion

[Xin Liu]

Hello,

I'm new with Gadgetron. I want to convert Siemens raw data to ISMRMRD format. A typical error with my files I encountered as following.

$ siemens_to_ismrmrd -f meas_meas_MID00832_FID217691_TF_MULTI_CINE_IPAT_RETRO_LAX.dat -o out.h5

Siemens file is: meas_meas_MID00832_FID217691_TF_MULTI_CINE_IPAT_RETRO_LAX.dat
Parameter XSL stylesheet is: IsmrmrdParameterMap_Siemens.xsl
Parameter map file is: IsmrmrdParameterMap_Siemens.xml
This file contains 1 measurement(s).
VD line file detected.
Protocol name: TF MULTI CINE IPAT RETRO LAX
Number of parameter buffers: 6
Buffer Name: Config
Buffer Name: Dicom
Buffer Name: Meas
Buffer Name: MeasYaps
Buffer Name: Phoenix
Buffer Name: Spice
Trajectory is: 1
Failed to find YAPS.lFirstFourierPartition array
center_line = 98
center_partition = 0
Baseline: N4_VD13A_LATEST_20120616
WARNING: End of file was not reached during conversion. There are 480 additional bytes at the end of file.

How can I do with this problem?

Thank you,
Xin Liu

[Xue, Hui (NIH/NHLBI) [E]]

Hi Xin,

 

The conversion seems completed without error. The warning at the end does not mean the failure of conversion. Do you get the out.h5?

 

Regards

 

Hui

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[Xin Liu]

Hello Hui,

Thank you for the quick answer. I have several files. Some will generate out.h5 file, some not. And the file size is small. I feel that some data lost. Each of my file conversions will have "Failed to find YAPS.lFirstFourierPartition array". I am attaching a data file which does not generate the out.h5 for your reference.

Bests,

Xin

在 2017年5月16日星期二 UTC-5下午6:25:17，Hui Xue写道：

[Xue, Hui (NIH/NHLBI) [E]]

Hi Xin,

 

I tried to convert the data and it did not produce .h5 file. When I tried to load this dat file to mdb, it complains for incomplete data. It looks like that this dat file is not correct. Did you twix it out from the scanner?

 

Regards

 

Hui

 

From: Xin Liu [mailto:uhliu...@gmail.com]
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Subject: Re: problem with siemens raw data conversion

 

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[Xin Liu]

Hi Hui,

I can not access the scanner directly. The data are provided by the operator. Is the instruction on this link http://www.nmr.mgh.harvard.edu/~greve/siemens-raw-save.html correct to retrieve raw data from the scanner? Thank you.

Best Regards,

Xin

在 2017年5月16日星期二 UTC-5下午7:21:10，Hui Xue写道：

[Xue, Hui (NIH/NHLBI) [E]]

Hi Xin,

 

The instruction is correct. Maybe operator triggered another saving before current one is completed ?  This will cause the current saved data incomplete.

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[Xin Liu]

Hi Hui,

I will confirm with him. Is the mdb a public avaible tool? Where can I get it? I do not have access to Siemens IDEA now. I am sorry that I have so many silly questions.

Thank you,

Xin

在 2017年5月16日星期二 UTC-5下午9:18:09，Hui Xue写道：

[Xue, Hui (NIH/NHLBI) [E]]

Hi Xin,

 

Yes, mdb is a tool with siemens idea. It can be used to open and browse through the siemens meas dat file.

 

If you don’t have access to mdb, you can convert siemens data to ismrmrd format and use the matlab toolbox of ismrmrd (in the matlab folder of ismrmrd package, g...@github.com:ismrmrd/ismrmrd.git, ismrmrd/matlab/+ismrmrd/) I found this toolbox is  very easy to use to access data in matlab. Examples are in the ismrmrd/examples/matlab/ folder).

 

If the data is exported correct, siemens_to_ismrmrd can almost always work. You can get the gadgetron integration test data which has quite some .dat files and try the conversion.

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[Xin Liu]

Hi Hui,

I can successfully convert the test data provided with Gadgetron. I will check with our operator. Thank you very much!

Best Regards,

Xin

在 2017年5月17日星期三 UTC-5上午8:30:04，Hui Xue写道：

[Xin Liu]

Hi Hui,

I confirmed that the operator used twix to retrieve the data. I am physically there to copy one raw data file today. I can convert it to ismrmrd format (still with same warning as previous file). But when I run the test_recon_dataset.m, I get following error.

>> test_recon_dataset

Subscripted assignment dimension mismatch.

Error in test_recon_dataset (line 134)

                K(:,ky,kz,:) = meas.data{acqs(p)};

I can use this matlab example file to reconstruct the Shepp-Logan phantom test datasets. Would you please take a look into it? I shared the data:

https://drive.google.com/open?id=0B1OdFtZbNErjOVRWN1RlMXkya00

Thank you!

Xin

在 2017年5月17日星期三 UTC-5上午8:30:04，Hui Xue写道：

Hi Xin,

[Xin Liu]

Hi Hui,

I think siemens_to_ismrmrd does not convert the complete raw data to ISMRMRD format data. The enc_Nx read from header is 512, but the data readin is 404. I am attaching the reconstruction result after I manually modify enc_Nx value.

Thank you,

Xin

在 2017年5月17日星期三 UTC-5上午8:30:04，Hui Xue写道：

Hi Xin,

[Xin Liu]

Hi Hui,

I found attached MATLAB file from https://github.com/cjohnevans/Gannet2.0 to be able to read the .dat file. Its NCol = 404. In siemens_to_ismrmrd converted file enc_Nx = 512. I am sorry that I am new in this area to have such silly questions.

Thank you,

Xin

在 2017年5月17日星期三 UTC-5上午8:30:04，Hui Xue写道：

Hi Xin,

[Hui Xue]

Hi Xin,

this data could have asymmetric echo acquisition. In this case, the readout len in ismrmrd will include the unacquired portion.

regards

Hui Xue

在 2017年5月22日星期一 UTC-4下午4:00:14，Xin Liu写道：

[Xin Liu]

Hello Hui,

Yes, you are right. Do you have a simple workround to use siemens_to_ismrmrd with such kind of raw data? Thank you.

Best Regards,

Xin

在 2017年6月6日星期二 UTC-5下午10:14:10，Hui Xue写道：

[Xue, Hui (NIH/NHLBI) [E]]

Hi Xin,

 

Here is a gadget to handle this: AsymmetricEchoAdjustROGadget

This gadget will pad the incoming readout line if asymmetric echo is used.

 

From the ISMRMRD_AcquisitionHeader, you can tell whether asymmetric echo is on or not by comparing the number_of_samples/2 and center_sample.

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