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MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
http://www.mrtrix.org
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Extracting phase encoding information from Philips data #1038

Open Lestropie opened 7 years ago

Lestropie commented 7 years ago

Finally got my hands on some Philips DICOM data, however I've been unable to find everything I need.

It looks like the water-fat shift per pixel is stored in 2001 1022. This can then be converted to an echo spacing via this equation; or similarly for the total readout time, which is what we want.

However I can't find anything indicating the sign of phase encoding. Siemens use an explicit CSA field PhaseEncodingDirectionPositive for this. Eye-balling the sample data I have, I can't spot any appropriate parameter contrast in the Philips headers between AP and PA data; having said that, there are also other unwanted differences between the image series I have, which makes it more difficult to find.

What would be ideal is if someone could acquire two consecutive protocols on Philips hardware, with only the phase encoding direction flipped on the second, so I can run a direct diff between the two dcminfo -all outputs.

Lestropie commented 6 years ago

Was given a link to this MatLab DICOM converter, which contains field names for many entries that are more-or-less empty in the MRtrix3 dictionary. Unfortunately 2005 107B "MRStackPreparationDirection" didn't give the result I had hoped; but it'd be worth nevertheless incorporating these field names into our dictionary.

egarza commented 6 years ago

Hi,

I work with Philips and it was hard to extract the information. People say the PAR/REC file has more information that the DICOM but I haven't confirm this.