Process Philips suppressed water DICOM files using command line

[Ping-Hong Yeh]

Hi Group, 

I  been trying to figure out using the command line to process Philips DICOM files, but not sure if there is a option for the "--format". I have used the "philips" but it looked for SPAR file.  There are options for DICOM or "Philips private DICOM" in the gui, but bot command line.  

Here is what i did, 

/Applications/Tarquin/tarquingui.app/Contents/MacOS/tarquin  --input /Users/twbrkmp4/Downloads/HBOT_presstest/HBOT1/original/data/MR/N-EVA-231_1/MR/s2D_PRESS_144_2301/1.3.46.670589.11.34102.5.0.1820.2014100315541.dcm --format  "philips" --fs 2000 --ft 1e6 --basis_csv /Applications/Tarquin/basis_sets/3_0T_basis --output_csv  /Users/twbrkmp4/Downloads/HBOT_presstest/output.csv --output_pdf /Users/twbrkmp4/Downloads/HBOT_presstest/output.pdf --output_xml /Users/twbrkmp4/Downloads/HBOT_presstest/output.xml

Thank you. 

Ping

[Martin Wilson]

Hi Ping,

Try "dcm" or "philips_dcm" as the format.

Martin

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[Ping-Hong Yeh]

Hi Martin, 

 It does not seem to work. I think the problem was not that dicom file may be the water reference file, but not the water suppressed one. 

Do you know if the dicom header has the tag to tell which one it is? 

Thanks. 

Ping 

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[Martin Wilson]

Hi Ping,

Afraid not. Philips DICOM (enhanced mode) tends to store the WS and W
data in the same file saved as two separate frames. Non
enhanced/proprietary Philips DICOM format may have the information,
but Philips don't publish a tag dictionary.

Martin

[Ping-Hong Yeh]

Hi Martin, 

 I have contacted a previous Philips MRI physicist and he said the dicom tag for MRS raw data is (5600,0020), which should contain both water-suppressed and water_unsuppressed data.

http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(5600,0020)

0 for MRSI and 1 for water reference. 

I wonder if Tarquin add this option for reading Philips dicom  files so users can benefit from this. 

Thank you so much. 

Ping

[Martin Wilson]

Hi Ping,

You are correct that tag (5600,0020) contains the raw MRS data points,
but I'm afraid it doesn't tell you if it is water-suppressed or not.
I'd be interested to know if there is another tag that you (or
Philips) think gives this information.

Martin

[Ping-Hong Yeh]

Hi Marin, 

 

 Thanks for the reply. 

You are correct that dicom tags in Philips MRSI data are not consistent throughtout  different versions. For  those acquired with version R.3.2 (the one i try to analyze), the private tag indicating "water" or "metabolite" was indeed stored in the ('2005', '1304') , where 0 is metabolite and 1 is water reference.  

Although standard DICOM MRS data should have  tag(5600, 0020) for water or metabolite, but it is not always the case. 

V/R, 

Ping