VisuCoreTransposition not corresponding to RECO_transposition in version 5.1

[SebastianoF]

VisuCoreTransposition should reflect the value of RECO_transposition. In some cases in version 5.1 this does not happen. This Bruker ParaVision feature, can cause problems in the re-orientation. (XY, switched with YX when RECO_transposition > 0). Some system to find the RECO_transposition from the visu_pars file alone needs to be found.
Thanks to @neurolabusc for pointing this out.

[gdevenyi]

Indeed, in the PV5.1 data I have VisuCoreTransposition doesn't exist in visu_pairs

I have lots of data and access to a PV5.1 manual and console, happy to share anything.

[neurolabusc]

Note images from @gdevenyi are already included with bruker2nifti_qa. I think a large dataset should allow a dedicated developer to decipher how the formats have changed over time and a stable method to extract spatial coordinates regardless of the vintage of the data. As a professional vendor, it is unfortunate that Bruker did not document this. If anyone wants to tackle this, they could generate a pull request to support this.

[gdevenyi]

I now have PV5 and PV6.1 on the same computer attached to the same MRI. I can conceivably do some head-to-head comparisons of the same sequences collected.

Any requests?

[SebastianoF]

Oh, well... Thanks!!
Do you think an example of a 2d and a 3d sequence with both versions for the same sample (where left and right are distinguishable) may be of some help for further testing?

We should also involve the bruker2nifti_qa maintainers in this, who may like to host the example with the current dataset (I raised an issue pointing at this page here).

Thanks again for the offer!

[SebastianoF]

Morning @gdevenyi,
Good news from the bruker2nifti_qa side. Please follow up on this thread. @naveau has good insight into possible sequences for comparisons.
Thanks!

[neurolabusc]

@gdevenyi might be nice to have diffusion images with one set where slices are aligned orthogonal to scanner bore and another where they are rotated. Would be nice to have the NIfTI files exported by ParaVision 360 1.1. I am hoping that Bruker is now able to convert their proprietary format directly to standard formats, obviating the need for 3rd party tools that rely on reverse engineering.

@cecilyen may also have ideas.

Do the Bruker files record if the participant was scanner prone versus supine? Do they encode whether the participant is a biped or a quadruped (similar to DICOM)? Since NIfTI expects coordinates in the frame of reference of the participant, this would be useful to know.

[naveau]

On PV6.0.1, the patient position is reported in these files :

subject: ##$SUBJECT_position=SUBJ_POS_Prone
1/acqp: ##$ACQ_patient_pos=Head_Prone
1/visu_pars: ##$VisuSubjectPosition=Head_Prone

The type of participant is reported here :

subject: ##$SUBJECT_type=Quadruped
1/visu_pars: ##$VisuSubjectType=Quadruped
1/pdata/1/visu_pars: ##$VisuSubjectType=Quadruped