Hi Neurostar experts,
I am currently trying to convert a DICOM dataset into BIDS format. The dataset was acquired with a Philips scanner.
I read in the dcm2niix Readme file that " While the Philips DICOM header distinguishes the phase encoding axis (e.g. anterior-posterior vs left-right) it does not encode the polarity (A->P vs P->A).Another value desirable for TOPUP is the “TotalReadoutTime”."
As both information are absent from the DICOM headers, how do people do to convert their Philips datasets into BIDS?
Thanks,
Best,
-Loïc
This is a limitation of Philips DICOMs, not dcm2niix. These parameters are not encoded in the Philips DICOMs. You will want to work with the MR physicist or the Philips Clinical Scientist associated with your site to determine these parameters. Not that the FSL definition of TotalReadoutTIme is not intuitive, as a partial Fourier scan should report the same effective readout time (in terms of distortion) as an otherwise full Fourier scan even though the physical readout time differs.
@sandeepganji may have some other ideas - in theory these parameters can also be derived from the exam card files (if these were preserved), but these use a proprietary format.
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Thanks for your reply.
I attached my examcard file to this new post. If somebody would be able to point out some variables that would help determine the phase encoding direction and the total readout time, I would appreciate that!
Thanks,
Best,
-Loïc
noise_20201117_2_.txt (491.0 KB)
Hi Idaumail,
My guess (based on comparison with my data and what I’ve been told at the scanner) is that:
EX_STACKS_0__prep_dir : AP
EX_STACKS_0__fat_shift_dir : A
Means anterior to posterior
EX_STACKS_0__prep_dir : AP
EX_STACKS_0__fat_shift_dir : P
Means posterior to anterior
Also this suggests my guess might be correct: JISCMail - FSL Archives
It’s just a guess in case it helps but the best would likely be to confirm with people who know for sure!
Annick