Description

This relates to the new flavor GE_PCASL_3Dspiral_DV25.0_1.5T_1.

This is the same DV25.0 product sequence flavor as we see all the time, but now acquired at 1.5T and the three volumes are concatenated as [CBF deltaM M0scan]. In the dcm2NII stage, this will issue a LabelingDuration conflict warning, and it then stores: "LabelingDuration":0.00145,. Both PostLabelDelay and InversionTime are detected but removed in our nii2BIDS.

Separate the [CBF] and [deltaM M0scan] in the DICOM stage fixes most issues, but the PostLabelingDelay is still not detected. And we should be able to handle a combination of [CBF deltaM M0scan], at least per BIDS.

NOTE FOR HENK: It works correctly now, though there are some smaller errors and warnings -> as noted above. I have added those to the list of minor flavor issues to fix. Added to #342

Warning: Difference in field LabelingDuration between merged JSONs
In xASL_bids_MergeNifti>xASL_bids_MergeNifti_Merge (line 636)
In xASL_bids_MergeNifti>xASL_bids_MergeNifti_GEASLFiles (line 258)
In xASL_bids_MergeNifti (line 78)
In xASL_imp_DCM2NII_Subject_SortASLVolumes (line 139)
In xASL_imp_DCM2NII_ConvertScan (line 181)
In xASL_wrp_DCM2NII_Subject (line 126)
In xASL_wrp_DCM2NII (line 45)
In xASL_module_Import (line 149)
In xASL_init_Iteration>runIteration (line 382)
In xASL_init_Iteration (line 125)
In ExploreASL_Import (line 50)
In ExploreASL (line 91)

Tasks

• For the notes below, please load the ExploreASL branch belonging to this issue and load the flavor #1294
• Is the PLD automatically removed?
• Correctly detect the aslcontext.tsv, now it detects [deltam deltam deltam] but this should be [cbf deltam m0scan]
• If I specify the ASLcontext in studyPar.json, the "DICOM value" [deltam deltam deltam] will overwrite my value in xASL_bids_BIDSifyASLJSON. The studyPar.json values should always have preference over DICOM values (in general)? We only add stuff to studyPar.jsonif we are really sure that the parameters are missing or wrong in the DICOM. This should be fixed.
  BTW: BIDS2Legacy works if I manually adapt the ASLContext.tsv in the rawdata.
• If we have CBF in ASL when splitting ASL and we also have deltam + m0scan, or also control+label, then we treat CBF as if it would have been a dummy scan in BIDS2Legacy
• The dummy scan position option is not working correctly. E.g., for FlavorDatabase/Siemens_PCASL_multi_VE11C_1/rawdataReference/sub-101/ses-1/perf/sub-101_ses-1_run-1_asl.json this is done incorrectly, as DummyScanPositionInASL4D is added to studyPar.json instead of dataPar.json, and thus ends up in the ASL sidecar (which is not according to BIDS). Moved this to Correct JSON when splitting M0 #1062

Release notes

Remove cbf as dummy when deltam/control/label are present in the timeseries.