Dummy volumes

[HenkMutsaerts]

Description

Dummy scans

If there are dummy scans inside the DICOMs/NIfTIs, they should be removed from the NIfTI. Then the NumberOfVolumesDiscardedByUser should be added with the number of volumes discarded.

(see also OASIS dataset: Siemens PASL 2D EPI)

• DICOM2BIDS (import module ExploreASL OR something else) -> at beginning scale slope check
• BIDS validator (needs to give no errors)
• Running ExploreASL ASL module -> at beginning scale slope check

QC steps (in BIDS2Legacy & in ASL module):

• Even number of volumes
• Automatic detection of control-label order
• Automatic detection of M0 validity
• NumberOfVolumesDiscardedByUser
• Check version that ASL data was imported with (giving warning if unknown)
• Can we put GeneratedBy in raw?

If scale slopes were already applied, this was a previous ExploreASL version.

_aslcontext.tsv should be adapted accordingly

Requirements

Optional: add feature requirements here

How to test

Optional: insert description about how to test the code changes here

Release notes

Required: summarize the changes for the release notes here

[BeatrizPadrela]

I was processing OASIS, and before the processing, I was already deleting the first volume (with the script to prepare the data before processing - CustomScripts), to keep the correct 104 volumes instead of 105 (this one extra is the dummy scan). However, during the ASL module, there's a check for this dummyscanposition, and it deletes again the dummy scan (103 volumes instead of 104):

So, either we remove the dummy scan before, or we just keep the dummy scan and add the field DummyScanPositionInASL4D. Because the SplitASL function receives an input called iDummy, xASL_io_SplitASL(inPath, iM0, iDummy), based on an x.modules.asl.dummy

Just fyi