I came across an issue with importing the phase encoding direction from my DICOM images.
I would like to generate an EDDY style acquisition parameters file when converting my DICOMs to NIFTI. I use the following command:
DICOM_SERIES='*b3000*' mrconvert DICOM/ dti.nii -export_grad_fsl dti.bvec dti.bval -export_pe_eddy acq_par.txt index.txt
When I compare the PE directions in the generated acp_par.txt file with those provided in the JSON file produced by dcm2niix (MRIcroGL) they match perfectly when the PE is A>>P or P>>A (eg. when JSON file says
j-, I get
0 -1 0 ... as the PE scheme in my acq_par.txt file)
However if the PE directions is L>>R or R>>L, the signs are opposite, eg. when the JSON file says
i- I get
1 0 0 ... in my acq_par.txt file and vice versa. I observed this for axial as well as for oblique acquisitions. When provided to FSL’s TOPUP, the MRtrix generated PE scheme produces wrong results, while the dcm2niix PE directions produce correct results.
We have a Siemens MAGNETOM Skyra scanner with E11E software. We are sending the HARDI data in Mosaic format to our PACS. From there we export the DICOMs.
Do you think this could be fixed?
Thank you very much in advance.
P.S.: The reason the polarity matters to me is that sometimes at our institution the main HARDI acquisition has PE direction A>>P while the supplementary b0 images intended for distortion correction have L>>R PE direction. TOPUP documentation on this:
However, if ones acquisitions have been performed with phase-encoding along different axes it is important to get the signs to correspond to the definition by your scanner manufacturer. (topup/TopupUsersGuide - FslWiki)
P.S.: Not sure whether it’s relevant, but just in case: When I used other software for spherical deconvolution (such as Explore DTI os StarTrack), I always had to change the sign of the x component of my BVECS file.